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Top 10 Hidden Islands in Indonesia for a Diving Trip

Indonesia, with its vast archipelago of over 17,000 islands, offers some of the world’s most spectacular diving experiences. While destinations like Bali, Komodo, and Raja Ampat are famous, numerous hidden islands remain unexplored by the masses.

These remote islands offer pristine coral reefs, vibrant marine biodiversity, and a truly authentic, off-the-beaten-path experience.

Whether you're an experienced diver or new to the underwater world, Uncharted Cruises provides exclusive access to these locations via private charter yachts and adventure liveaboards.

Here’s a guide to the top 10 hidden islands in Indonesia for diving enthusiasts:

1. Pisang Island – A Secluded Gem in South Halmahera

Pisang Island, located in South Halmahera, is one of Indonesia's hidden gems, offering pristine coral reefs and crystal-clear waters. Its remote position in the northern part of the Maluku Archipelago keeps it free from mass tourism, making it a diver’s paradise.

  • What makes it special: This secluded island is home to vibrant coral gardens and a rich biodiversity, making it perfect for divers seeking an untouched, tranquil environment.
  • Marine Life Highlights: Expect to encounter barracudas, reef sharks, Napoleon wrasse, and schools of jacks. The nutrient-rich waters also attract manta rays, turtles, and a variety of macro critters such as nudibranchs and seahorses, along with other reef fish like butterflyfish, triggerfish, and parrotfish.

Tip: Explore Pisang Island as part of a custom liveaboard Halmahera itinerary or combine it with other hidden locations in Eastern Indonesia.

2. Tidore Island – The West Halmahera Paradise

Located off the coast of West Halmahera, Tidore Island offers a pristine diving experience combined with rich cultural exploration. The island remains under the radar, ensuring an undisturbed diving environment.

  • What makes it special: Tidore is ideal for divers and non-divers alike. Its diving sites are secluded, offering vibrant marine life. On land, Tidore’s sleepy towns, mountain villages, and rich spice heritage offer a cultural experience.
  • For Non-Divers: Tidore’s capital, Soasio, offers scenic views from nearby forts and a chance to immerse in local life. Experience traditional architecture, visit spice plantations, or hike the slopes of Kie Matubu mountain for a unique blend of nature and culture.
  • Marine Life Highlights: While dive information is limited, Tidore’s remote waters offer abundant marine species. Dive sites are enriched with the occasional pelagic species and vibrant reef life.

3. Koon Island – The Fish Explosion Hotspot

Located in the Maluku province of Indonesia, Koon Island is known for its remarkable underwater scenes, where vast schools of fish swirl around the reefs in a breathtaking display. This site is even nicknamed “Too Many Fish” due to the overwhelming abundance.

  • What makes it special: The island’s remote location and lack of infrastructure make it a diver’s paradise. Its underwater spectacle includes schools of barracudas, jacks, and tunas, creating an unforgettable experience for photographers and marine life enthusiasts.
  • Marine Life Highlights: Expect to encounter mantas, reef sharks, Napoleon wrasse, and an array of macro critters such as nudibranchs and seahorses.

Tip: Koon Island is best explored as part of a liveaboard Banda Sea itinerary or fully customized Eastern Indonesia route.

4. Manuk Island – The Volcanic Wonder with Sea Snakes

Known as Snake Island, Manuk Island is located in the Banda Sea, offering a unique diving experience with its volcanic terrain and sea snake population.

  • What makes it special: Manuk Island’s volcanic origins shape its underwater topography, featuring walls, slopes, and pinnacles, while its sea snake population sets it apart as a unique destination for divers. The active volcanic backdrop adds to the adventure.
  • Marine Life Highlights: Along with sea snakes, you’ll encounter butterflyfish, damselfish, clownfish, moray eels, and parrotfish. Pelagic visitors include reef sharks and Napoleon wrasse.

5. Togean Islands - Remote Reefs and Coral Gardens

The Togean Islands, located in the Gulf of Tomini, are renowned for their untouched reefs and diverse marine species. These islands offer an unforgettable diving experience in one of Indonesia’s most pristine regions.

  • What makes it special: With its clear waters and diverse marine life, the Togeans are a diver's paradise. You’ll explore protected reefs, swim with jellyfish in Mariona Lake, and experience the region’s rich biodiversity.
  • Marine Life Highlights: Encounter moray eels, turtles, barracuda, and stunning coral reefs. The Togeans are also famous for swimming with jellyfish in Mariona Lake, where the creatures have lost the ability to sting.

6. Lucipara Islands – Pristine and Uninhabited

The Lucipara Islands, located in the middle of the Banda Sea, are uninhabited and rarely visited, offering some of Indonesia's most pristine dive sites.

  • What makes it special: Surrounded by clear turquoise waters, these uninhabited islands provide the perfect destination for divers seeking a true off-the-grid experience. The area features steep drop-offs, lagoons, and vibrant coral gardens.
  • Marine Life Highlights: See sea turtles, giant trevally, dogtooth tuna, and reef sharks. The waters are also home to juvenile grey reef sharks, barracudas, and an impressive variety of macro life such as seahorses and nudibranchs.

Tip: Accessible as part of a liveaboard Banda Sea or customized Eastern Indonesia adventure.

7. Selayar Island – Off the Beaten Path

Located in South Sulawesi, Selayar Island offers pristine beaches, diving hotspots, and cultural experiences.

  • What makes it special: Selayar is a unique mix of natural beauty and rich culture. The island is home to the Takabonerate National Park, known for its diving and snorkeling, and remote villages that preserve local traditions.
  • Marine Life Highlights: Dive sites here feature schools of jacks, barracudas, and manta rays. Snorkelers and divers can also explore vibrant coral gardens and abundant reef life.

Tip: Selayar Island is ideal for exploration via a private charter yacht offering flexibility to discover both the island’s underwater beauty and its cultural landmarks.

8. Alor Island – Macro Diving Paradise

Alor Island, in East Nusa Tenggara, is famous for its vibrant reefs and exceptional macro diving. This hidden gem attracts underwater photographers and divers seeking rare macro critters.

  • What makes it special: Alor’s nutrient-rich waters support a variety of habitats, from large pelagic species to tiny macro critters. The island's diving sites offer dramatic landscapes, healthy reefs, and exciting drift dives.
  • Marine Life Highlights: Encounter pygmy seahorses, mantis shrimp, and nudibranchs, along with schools of barracudas, giant trevallies, and occasional reef sharks.

Tip: Best explored via a liveaboard Alor, but also available for full private charter yacht itineraries across Eastern Indonesia.

9. Pantar Island – Remote Diving Experience

Situated between Alor and Flores, Pantar Island offers seclusion, healthy coral reefs, and rich biodiversity for a unique diving experience.

  • What makes it special: This remote island is perfect for experienced divers seeking solitude and a rich variety of dive sites. With clear, warm waters and a diverse marine ecosystem, it promises a peaceful, rewarding diving experience.
  • Marine Life Highlights: Dive among schools of snapper, parrotfish, moray eels, barracudas, and encounter mantas, reef sharks, and Napoleon wrasse.

Tip: Accessible as part of an adventure liveaboard route or fully customized Eastern Indonesia itinerary.

10. Morotai Island – An Untouched Diving Destination

Located in northernmost Indonesia, Morotai Island remains one of the least developed dive spots, offering pristine diving experiences and historical wreck sites.

  • What makes it special: Morotai offers clear waters, vibrant marine life, and World War II wrecks, making it a unique destination for divers seeking history and adventure.
  • Marine Life Highlights: Expect to encounter manta rays, turtles, reef sharks, and a variety of reef fish. Historical wrecks add an exciting element to your dive.

Tip: Morotai is best explored via a private charter yacht or adventure liveaboard, offering flexibility and access to the island’s pristine dive sites.

Why Choose Uncharted Cruises for Hidden and Exploration Diving

KLM Thalassa 42 ready to explore Indonesia hidden islands

While these islands may seem like the ultimate off-the-grid getaway, they’re not always easy to reach. That’s where Uncharted Cruises comes in.

Uncharted Cruises specializes in private charter yachts and adventure liveaboards, offering expert guidance and flexible itineraries across all of Eastern Indonesia.

Whether it’s liveaboard Halmahera, liveaboard Banda Sea, liveaboard Alor, liveaboard Raja Ampat, or fully customized routes to remote hidden islands, you can explore at your own pace.

Our team combines expertise in marine biodiversity, safety, and adventure, ensuring that every trip is an unforgettable experience, whether for large groups, private charters, or individual explorers.

Ready to Explore Indonesia’s Hidden Diving Gems?

From the untouched reefs of the Banda Sea, Halmahera and beyond, Uncharted Cruises can craft a private charter yacht or adventure liveaboard itinerary tailored to your dream adventure.

Contact our team today to plan your next Eastern Indonesia diving expedition. Don’t just read about these hidden wonders, experience them with Uncharted Cruises.

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