12-Day Philippines Nature Tour to Palawan Island, Cebu City, Apo Island & Bohol Island from Manila

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Tour starts
Manila, Metro Manila, Philippines
12 days
Ending place
Manila, Metro Manila, Philippines
Minimum age:


Go on a scenic countryside tour and try outdoor activities like trekking and snorkeling across Palawan, Cebu, Apo Island, and Bohol with this 12-day vacation package. For your convenience, this trip includes roundtrip flights from Manila, land/ferry transfers, and accommodation.

Traverse the cobblestone streets of Intramuros, one of the earliest districts in Manila. Then, get a glimpse of the Spanish colonial period while admiring old fort ruins and churches. Afterward, you will board a plane to Panglao International Airport from Manila. 

In the Bohol countryside, you will cruise along the jade-green waters of the Loboc River. You will also visit the stunning geological formation at the Chocolate Hills. Then, you will explore the University town of Dumaguete. Visit Silliman University, the first American-Protestant university in the Philippines and Asia.

Your Dumaguete tour continues at Apo Island. Get the rare opportunity to swim with turtles. Then, head next to Kawasan Falls in Cebu and experience an unforgettable canyoneering adventure. You will also explore the Temple of Leah, known as Cebu’s Taj Mahal. Then, see colorful blooms at Sirao Flower Farm, Cebu’s little Amsterdam.

From Cebu, you will take a short flight to Puerto Princesa. You will go on an island-hopping tour to Starfish Island, Luli Sandbar, and Cowrie Island in Honda Bay. Afterward, you will traverse a UNESCO World Heritage Site, the Puerto Princesa Underground River. 

Then, you will escape to Port Barton’s tropical islands in San Vicente, Palawan. Laze on white-sand beaches and sink your feet into its clear waters. Then, conclude your Palawan tour in El Nido’s Big Lagoon. The towering limestone cliffs will welcome you upon arrival.

Get a well-deserved dream getaway to the Philippines with this 12-Day tour to Palawan, Cebu, Apo Island, and Bohol from Manila. Check availability by choosing a date.

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11 nights accommodation (budget category)
11 days breakfast
11 lunch
All flights with 20kgs baggage allowance
Day 1 - Intramuros Tour (Manila)
Day 2 to 7 - Bohol, Dumaguete and Cebu Tour (Central Visayas)
Day 8 to 11 - Puerto Princesa, Port Barton and El Nido Tour (Palawan)
Day 12 - Back to Manila
All transportation to and from included activities and destinations
All environmental fees, port fees, and all other applicable taxes


Island Hopping
Culture, Arts & Historical Tours

Daily itinerary

Day 1
Sunrise over Fort Santiago in Intramuros

Day 1 - Day 1: Intramuros Tour

Upon arriving at Ninoy Aquino International Airport, your private van will fetch you and take you to your hotel in Manila or near Roxas Boulevard. You will head to your first stop, the walled city of Intramuros. Witness marvelous structures, museums, and century-old churches lined up on its cobblestone streets. Your first destination is the ruins of Fort Santiago, an old fortress and prison cell for political prisoners during the Spanish era. Our national hero Jose Rizal was imprisoned here before his execution in Bagumbayan. At Plaza Roma, you will set foot on one of the three major public squares and trade centers in Intramuros. Up next is Bahay Tsinoy, which features the life and contribution of ethnic Chinese to Philippine history. Meanwhile, Casa Manila is an 1850s Bahay-na-Bato replica depicting the affluent colonial lifestyle of Illustrados. Afterward, you will stroll along the walkways in San Diego Gardens. Just across the garden, you will see Baluarte De San Diego, a 16th-century bastion. You will enter the iconic San Agustin Church and Museum, which houses a bamboo organ and the hidden mausoleum of Miguel Lopez de Legazpi. Lastly, step inside Manila Cathedral’s grand facades to see the grand episcopal throne of the Archbishop of Manila.
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Day 2
Chocolate Hills in Bohol

Day 2 - Day 2: Bohol Countryside Tour

On Day 2, you will head to the Visayas via Panglao International Airport. Upon arrival at the terminal, your van will take you to your hotel in Panglao, Bohol. Then, you will head to your first destination, the Corella Tarsier Sanctuary. You will see one of the smallest primates, known as Tarsiers. Avoid using the flash of your cameras because they are highly sensitive to light. After touring around the tarsier sanctuary, you will hop aboard a floating restaurant that will cruise along the jade-green waters of the Loboc River. Up next is Baclayon Church, a National Cultural Treasure founded in the 17th century. It is one of the oldest churches in the Philippines. However, it got destroyed after a magnitude 7.2 earthquake that hit Bohol in 2013. Its renovation was fully completed in 2018. Afterward, you will proceed to the laid-back town of Bilar. You will visit Butterfly Conservatory, Bohol’s first butterfly breeding and conservation site. Your second stop is Bilar Forest, a 2km-long forest with tall mahogany trees. Finally, you will visit a stunning geological formation at the Chocolate Hills. It features over 1,000 hills that turn brown during summer and green come the rainy season.
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Day 3
Aerial view of Pamilacan Island in Bohol

Day 3 - Day 3: Pamilacan Island Tour

The next leg of your Bohol escapade continues at Pamilacan Island. You will leave early from your hotel in Panglao to take a short boat ride to the island. Pamilacan Island is nestled at the heart of the Bohol Sea. Home to hundreds of marine species, the island shelters a wide variety of aquatic creatures like bucket sponges, moray eels, and sea snakes. You may also see occasional sightings of whales and dolphins on your way to the island. Once you arrive, you will get a rare opportunity to swim with green sea turtles. At present, only less than 1,500 residents are inhabiting Pamilacan Island. In the 90s, the locals relied on whale and manta ray hunting as their source of livelihood. However, the government put an end to this illegal practice, so the locals relied on promoting local tourism on the island. Snorkeling and diving are some of the must-try activities for ultimate adrenaline. While navigating the vast seascape, you will discover majestic underwater sanctuaries. In the afternoon, you can lounge on the white sand or head to Pamilacan Watchtower to catch the sunset. The Spaniards used it as a lookout tower to check if there are pirates nearby.
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Day 4
Rizal Boulevard in Dumaguete

Day 4 - Day 4: Dumaguete City Tour

Take a short flight to Dumaguete-Sibulan Airport from Bohol on the 4th day of your vacation. Dumaguete City is a premier educational spot in Visayas and Mindanao. It is also known as the City of Gentle People. One of the prestigious colleges here is Silliman University. It is the first American-Protestant university in the Philippines and Asia. The campus boasts a university zoo and a research facility. Then, you will proceed to downtown Dumaguete. You will drop by the iconic structure of St. Catherine De Alexandria and the historical Dumaguete Campanario. Then, you may opt to buy fresh seafood at Dumaguete Public Market. Afterward, you will visit the nearby Provincial Capitol and Freedom Park. At Claytown Pottery, you can purchase unique souvenir items, including handmade pots. You can also buy novelty items at Sidlakang Negros Village. Then, you will drop by Lab-as Seafood to take your lunch break. At the Valencia Forest Camp, you will gaze at scenic and lush landscapes. Next is the Cata-al War Museum, where you will browse through World War II artifacts. Then, you will pay a short visit to San Agustin de Hippo Church in Bacong town. Lastly, you will drop by the Negros Oriental Arts and Heritage Center to purchase last-minute keepsakes.
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Day 5
Apo Island in Dumaguete

Day 5 - Day 5: Apo Island Tour

On Day 5, you will ride a boat to Apo Island, around 25km away from Dumaguete. The boat ride takes more or less 40 minutes. You will find the island at the southeastern tip of Negros Island. Apo Island is a protected marine habitat that boasts rich underwater sanctuaries. In the Visayan language, the name “Apo” means elderly or respected ancestor. Apo Island is one of the top diving and snorkeling spots in the Philippines. This volcanic island covers 74 hectares of land area. It shelters over 400 coral species and 650 documented fish species. The locals implement strict eco-tourism practices that tourists must follow to ensure the protection and preservation of the island. The stunning blue waters will welcome you upon arriving at Apo Island. Take a refreshing dip and dive deep to see different aquatic creatures, including tunas and manta rays. You may even get a chance to swim with sea turtles at Turtle Point. Before the end of your Apo Island tour, you can go trekking to the 600-meter Habagat Eco-Trail. Here, you will see a panoramic view surrounding mountains and natural rock formations. Afterward, you will head back to your hotel in Dumaguete.
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Day 6
Aerial view of Kawasan Falls in Cebu

Day 6 - Day 6: Kawasan Falls & Moalboal Sardine Run Tour

Go on a canyoneering escapade on the 6th day of your vacation. You will head to Badian, Cebu via a ferry and van transfer from Dumaguete. Once you reach Badian River, you will scramble and crawl through the slippery rocks along the beautiful gorges and river canyons. You will soon arrive at the three-tiered Kawasan Falls. Jump off the cliff as high as 30 feet and plunge into its emerald blue waters. You can also dip into the natural pools and lagoons surrounding the enchanting falls. After your heart-pounding adventure, you will ride a boat to reach the world-class diving sites at Moalboal. The beautiful coastal town boasts stunning coral gardens and a wide variety of marine species. Witness the magnificent sardine run at Pescador Island. You will swim with countless sardines merging in perfect unison. The main point of interest for divers is the underwater cave, known as The Cathedral. You will swim through cave exits as deep as 18 meters. After your dives, you can lounge at the nearby Panagsama Beach. Then, you will swim with sea turtles and other colorful exotic fishes on Turtle Island. At the end of your Moalboal tour, you will return to your hotel.
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Day 7
Sirao Flower Farm in Cebu

Day 7 - Day 7: Cebu City Tour

Your Cebu adventures will continue in its city attractions. Your private van will take you to your first stop, Taoist Temple. It features beautifully preserved Chinese architecture, specifically the Great Wall of China’s replica with dragon statues. The hilltop temple also has a souvenir shop on-site. Your next stop is downtown Cebu. Basilica Minore Del Santo Nino is the country’s oldest Roman Catholic church. You can find the iconic Magellan’s Cross a few meters from the church. It was established to commemorate Magellan’s expedition to Cebu in 1521. Then, you will proceed to the Heritage of Cebu Monument. It is a tableau of concrete and bronze-made sculptures featuring Spanish galleons and other relevant figures. It also symbolizes significant events in history, including the Battle of Mactan. Well-known figures like Sergio Osmena, the 4th President of the country, are also featured here. Up next is Yap-San Diego Ancestral House, a 17th-century Chinese settlement. It is believed to be the first Chinese house built outside of China. You will also marvel at the Temple of Leah or Cebu’s Taj Mahal. Lastly, you will visit Sirao Flower Farm to see colorful blooms. This majestic flower plantation is also named Cebu’s Little Amsterdam.
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Day 8
Aerial view of Cowrie Island in Puerto Princesa Palawan

Day 8 - Day 8: Puerto Princesa Honda Bay Island Hopping Tour

From Cebu, you will board a plane to Palawan via Puerto Princesa International Airport on your 8th day of vacation. You will go on an island-hopping tour to the majestic islands dotting Honda Bay in Puerto Princesa, Palawan. Your private van awaits you at the airport terminal. Upon arrival, you will proceed to your hotel in Sabang. Then, you will ride a boat to reach the clear blue waters and white-sand beaches of Honda Bay. Puerto Princesa is the only coastal city in Palawan that serves as its provincial capital. Here, you will find the jump-off point of the boat trips heading to Honda Bay. Your first stop is at Starfish Island, home to an array of colorful starfishes. One of which is the perfectly symmetrical five-armed orange starfish. You can also spot other marine species, including pufferfishes and yellowtail snappers. Up next is the boomerang-shaped Cowrie Island. It is considered the largest one among the three islands. Here, you can try various water activities like snorkeling and banana boat riding. Your last stop is Luli Island’s powdery white sandbar. The sandbar submerges at low tide and reappears again during high tide. There are also floating hammocks throughout the bay.
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Day 9
Tourists going inside Puerto Princesa Underground River

Day 9 - Day 9: Puerto Princesa Underground River & City Tour

Spend your last day in Puerto Princesa by cruising along the famous UNESCO World Heritage Puerto Princesa Underground River. From Sabang Boat Terminal, you will ride a boat to Puerto Princesa Subterranean River National Park. The Puerto Princesa Underground River is a majestic limestone karst landscape that was recently recognized as one of the New 7 Wonders of Nature. It is 8km long and emerges directly to the sea. Upon entering its underground cave system, you will witness its spectacular ‘mountain-to-sea’ ecosystem and rich biodiversity. After your river tour, you will head to the city proper. Your first stop is at Baker’s Hill, where you can purchase baked goodies and local pastries. Then, you will head to Plaza Cuartel. It is a former Spanish garrison and penal colony that has become a leisure park. Your next stop is Palawan Wildlife Rescue and Conservation Center, research center, and breeding facility. It houses saltwater crocodiles, one of the critically endangered species in Palawan. For your last activity, you will hike up Mitra’s Ranch. It sits atop a hill overlooking a panoramic view of the city. At the end of your tour, you will drop by Puerto Princesa Baywalk to catch the sunset.
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Day 10
Aerial view of a white sand beach in Port Barton Palawan

Day 10 - Day 10: Port Barton Island Hopping Tour

On Day 10, you will go island-hopping to Port Barton in San Vicente, Palawan. Just like El Nido, Port Barton features white-sand beaches and clear blue waters. It is a must-visit tropical paradise for travelers who like to veer away from the crowded spots in El Nido. Your first stop is Inaladelan Resort, a lovely glamping resort that sits on a 12-hectare private island. Before, it was called German Island until the locals renamed it after Inaladelan, which means motherland. You can also take advantage of the various sports facilities on-site. You can kayak, play beach volleyball, or set up a picnic by the beach. Every January, the turtle hatching season happens in Port Barton. If you happen to visit the island during this time, you may want to participate and help baby turtles take their first steps toward the ocean. Up next is Luli Sandbar, a piece of powdery white sand that appears during high tide. Then, you will explore the turtle snorkeling site. Here, you can swim with sea turtles. Meanwhile, you will see a wide variety of colorful fishes at the fish snorkeling site. After your island-hopping tour, you will head back to your accommodation.
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Day 11
Aerial view of Miniloc Island in El Nido

Day 11 - Day 11: El Nido Island Hopping Tour

Escape to the world-class islands of El Nido on your 11th day of vacation. You will go on an island-hopping tour to visit the stunning limestone cliffs and the finest lagoons dotting Bacuit Bay. To get there, you have to take a short boat ride. First, you will enter the Big Lagoon. To get inside, you need to pass through a steep and narrow entrance. The jaw-dropping landscape of the towering limestone formations awaits you inside. You will visit another breathtaking island in El Nido, the Miniloc Island. It is also a famous diving spot that features colorful and magnificent marine sanctuaries. Beneath its postcard-worthy beachscape, you will discover an evergreen forest. Your next stop is the Secret Lagoon. Unlike the Big Lagoon, it has a steeper and smaller entrance. The Secret Lagoon boasts a beautiful and unspoiled beach. Up next is Seven Commandos Beach, a palm-edged beach with tall coconut trees and lush mountains. Lastly, you will snorkel around the beautiful and impressive coral gardens at Shimizu Island. You can strike a pose behind the stunning rock formations and limestone cliffs as your backdrop. You can also swim and snorkel to discover its hidden underwater wonders.
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Day 12
Manila sign in a road near the airport

Day 12 - Day 12: Departure to Manila

It’s time to leave Palawan on the last day of your 12-day vacation. Pack up your things and wait for your van to pick you up from your hotel. Then, you will board a direct flight to Ninoy Aquino International Airport. You will head back to where you started, Manila.
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What to bring

Face mask and Face shield
Extra Clothes
Passport (Valid for 6 months from date of departure)
Swimwear and sunblock
Personal medicines

Good to know

Please bring appropriate clothing. Please be aware that your itinerary may have to be rearranged to fit your arrival date and time better.

All our guides speak English. For other languages, contact us for availability and rates.

Not all establishments accept credit or debit cards, and ATMs can be limited.

The season for dolphin watching in Dumaguete is from March to October and is subject to weather and wind conditions. If off-season or on days when the northeast monsoon is strong, dolphin watching may not be possible. During Habagat/ Southwest monsoon Season (June-October), boat ride to Apo Island may be rough.

In El Nido island hopping tour mandatory environmental fee and/or user’s see is to be paid directly in cash to the service provider in El Nido, The tour itinerary is subject to change based on weather and tidal conditions. Tours will start only once operators are given permission to sail by the Local Government Unit (LGU) and the Philippine Coast Guard. Delays in start of tours or cancellation of tours affected by this is beyond the service providers’ control.

Limitation to the number of tourists, boats, kayaks and time of stay in El Nido lagoons are strictly enforced by the PAMB. Secret Beach, Big Lagoon and Small Lagoon are no longer allowed to be toured on the same day as part of the policies of the Protected Area Management Board (PAMB) of El Nido.

A mandatory user fee of PHP 200 per person is collected by PAMB for every entry to the Secret Beach, Big Lagoon and Small Lagoon.

Single use-plastics are banned in El Nido island tours. Please bring reusable water bottles or tumblers. All visitors are required to bring their own trash back to the boats.

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See our accommodation levels below and our preferred accommodation partners under each day in the daily itinerary. All accommodation levels, bookings for one person will be arranged in single rooms, bookings for two or more people will share a twin/double, and odd number groups will always be allocated a single room. If you are travelling in a group, but prefer a single room, please make separate bookings. Teenagers and children will be arranged in the same room with parents. If additional room(s) is needed, additional costs will incur.

For multi-day guided tours, accommodation cannot be upgraded and the levels below do not apply. Guide to the Philippines will provide you with the best available accommodation at the time of your booking from our preferred partners. If our preferred partners are fully booked at the time of your booking, we will find another suitable accommodation for you of similar level.

We always do our best to accommodate special requests, which may incur additional costs. Press choose a date to find availability.


Private rooms with private bathrooms in guesthouses or small hotels with basic amenities.


Private Rooms with a private bathroom at three-star hotels or resorts located in the city center, in close vicinity, or near the beach area. Breakfast is included and with basic room amenities and toiletries.


Rooms at four-star to a five-star hotel in the city center or beachfront resort with a private bathroom at the absolute best locations with the best amenities, facilities, and services.

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