An Indonesian island peak with a stairway hiking trail along the ridge and a small ship anchored off the coast line.

1. Understand Your Ship Options

Numerous small ships of varying sizes and styles sail Indonesia. You can go the way of day boats, but selecting a first-class, seaworthy and safe vessel is of the utmost importance among these far-flung island chains. Thus, we highly recommend going beyond the day-tour circuit to more remote reaches via expedition ships. In Indonesia, our partner vessels range from classic wooden schooners that lend an authentic, romantic vibe to state-of-the-art expedition vessels that travel farther, faster with all the latest gear. Knowing your preference for ship style, activities and amenities will help narrow down your cruise choices.

A small sailing ship with raised sails.

2. Think About the Indonesia Wildlife You Wish to See

While wildlife encounters can never be guaranteed, seeking out endemic creatures is half the fun of adventure travel anywhere. In Indonesia, you can set your sights on Komodo dragons, birds-of-paradise and manta rays, among other exciting animals, but there are geographical nuances to consider.

A Komodo dragon with his tongue sticking out.

Traveling around the Wallace Line is a thrill for naturalists as it’s one of the most distinctive biogeographic areas on Earth.

Indonesia is famous for the Wallace Line, a faunal boundary separating two eco-zones (Asia and Wallacea, the transitional zone between Asia and Australia). The “line” was drawn by naturalist Alfred Russel Wallace in 1859 and runs between Borneo and Sulawesi down to the strait between Bali and Lombok. Traveling around this line is a thrill for naturalists as it’s one of the most distinctive biogeographic areas on Earth. West of the line you will find larger terrestrial mammals (tigers, elephants, orangutans), and east of the line look for marsupials, Australian cockatoos and birds-of-paradise. The Indonesian island of Sulawesi is an interesting exception to the Wallace Line with black macaques, pigs and tarsiers.

A sea turtle swimming by a snorkeler in the bright blue ocean water of Indonesia.

Komodo and Rinca Islands are the islands to visit if you are keen to see Komodo dragons. Snorkeling near Flores Island will offer you the best chance to see manta rays and sea turtles in deep currents, and some Raja Ampat routes hone in on the best chances to spot birds-of-paradise. Essentially, if you have an animal interest, there is likely an Indonesia cruise our team at AdventureSmith Explorations can connect you with. And whichever way you go, you can always return to see the full diversity of wildlife that Indonesia offers.

3. Clue into Seasonality

Indonesia cruises are available every month of the year, but ships often follow the trade winds and weather patterns to sail certain locations during their drier, less-windy months. For example, if you are seeking to sail Raja Ampat, plan your trip in the winter months (roughly, October through February). If your course is set on a Bali cruise, you can look for most sailings running from March through September.

Two mean in canoes navigating the shallow shoreline waters of Indonesia.
A row of palm treas and a canoe on a beach in Indonesia.

4. Choose Your Indonesia Island or Region

At nearly 750,000 square miles, Indonesia is the world’s largest island country and the seventh largest by combined sea-and-land area. Unless you have unlimited time, you simply cannot sail/see it all in one cruise itinerary. Thus, understanding the regions and knowing what you want out of your travel experience are paramount. Here is a brief primer:

Lesser Sunda Islands: Flores, Komodo & Bali Cruises

The most popular cruise itineraries are located in the Lesser Sunda Islands, perhaps due to the international airport on Bali and the island being a household name in travel thanks to its many established resorts. From west to east, the Lesser Sunda Islands comprise Bali, Lombok, Sumbawa, Flores, Sumba, Timor, the Alor archipelago, the Barat Daya Islands and the Tanimbar Islands, with the most common expedition cruise routes sailing regularly between Bali and Flores.

Each of these islands are different in their own right with myriad earthy highlights including volcanoes, rainforests, waterfalls, mangroves, white-sand beaches and even savannah.

Each of these islands are different in their own right with myriad earthy highlights including volcanoes, rainforests, waterfalls, mangroves, white-sand beaches and even savannah. This diverse landscape also holds a variety of wildlife that includes Komodo dragons  (Rinca & Komodo Islands) and manta rays in the deep channels that separate the Indian Ocean from the Pacific. Traditional lifestyles, quiet coastal villages, tribal rituals and intriguing ancestral traditions are also a major draw for travelers to the Lesser Sundas.

Local villagers performing a tribal dance ritual on an island in Indonesia.

Raja Ampat Cruises

For travelers looking for an immersive experience into the natural world of Indonesia, a cruise through the archipelago of Raja Ampat is the ideal modality. Located right in the heart of the Coral Triangle, this biodiverse area contains 450 species of reef-building coral, 1,400 species of fish and intriguing endemic sea life—the stingless jellyfish of the brackish interior lakes being the perfect example.

This kaleidoscopic underworld is ideal for the avid diver or snorkeler and pairs nicely with the stunning karst islands and unique bird life.

This kaleidoscopic underworld is ideal for the avid diver or snorkeler and pairs nicely with the stunning karst islands and unique bird life, including striking birds-of-paradise. The island biogeography of these birds helped Alfred Russel Wallace formulate his theories of speciation, much like the finches of the Galapagos did for Charles Darwin. Additionally, voyages in Raja Ampat offer adventures hiking, exploring caves and inner-island jungle walks to stunning waterfalls.

A small ship anchored in turquoise waters among several islands in Indonesia.

New Guinea Cruises (West Papua & Papua New Guinea)

While West Papua is technically the only territory of Indonesia, the island of New Guinea is often an itinerary stop or embarkation point for many Indonesia cruises. Many Raja Ampat cruises begin their journey in West Papua out of Sorong. Like its neighbor Raja Ampat, New Guinea is a hotspot for birds-of-paradise, but even more so as all but two genera are found here. At their core though, trips to New Guinea are truly cultural, offering a look into a world that very few outsiders see.

Trips to New Guinea are truly cultural, offering a look into a world that very few outsiders see.

West Papua and Papua New Guinea cruises highlight remote villages, traditional art and authentic rituals providing human connection with peoples that are living a very similar life to their grandparents, quite the feat for the twenty-first century. Papua New Guinea is also home to stimulating World War II history and is dotted with historic places of interest, monuments and tributes honoring the fallen. The colorful biodiversity of the underwater world delivers the perfect balance to days filled with culture and history.

Local village children dressed in tribal wear in Indonesia.

Spice Islands Cruises

Indonesian Spice Islands cruises offer a unique historic experience and deep cultural interactions among beautiful islands. The Spice Islands were mapped on ancient trade routes long before the Europeans even began searching out the Islands’ nutmeg, cloves, mace and pepper. The Portuguese, the first Europeans to start trading spices on a large scale from the Spice Islands in 1598, cornered the market for almost 80 years, infusing the area with Portuguese culture.

Indonesian Spice Islands cruises offer a unique historic experience and deep cultural interactions among beautiful islands.

The clashes between the varying nations and cultures in the region for centuries offers a fascinating historic journey that can capture any traveler’s imagination. Remnants of this highly utilized trade route are still seen today on Spice Island cruise itineraries that also can include snorkeling with whale sharks; exploring lush national parks; visits to traditional villages, colonial forts and palaces; and ideal snorkeling, diving and underwater adventures.

Various local spices set out in bowls at a market in Indonesia.

Sulawesi Cruises

Sulawesi, the Indonesian island east of Kalimantan (Borneo) and west of Raja Ampat, is perhaps the most unknown gem of the country’s many islands. Its shorelines and atolls are freckled with human settlements that rarely see tourism, so this is a land of true adventure travel and modern cultural experiences. Villages here are authentic working/living places for a variety of locals who make their living farming and fishing. This includes the nomadic Bajau people, commonly called the sea gypsies.

The unique shape of Sulawesi into several long peninsulas offers coral reefs alongside unique coastal geography ranging from steep mountains to palm-lined beaches.

The unique shape of the island into several long peninsulas offers coral reefs alongside unique coastal geography ranging from steep mountains to palm-lined beaches. The Togean Islands offer chances to swim with stingless jellyfish, and keen eyes should look for tarsiers and macaques. Sulawesi is also home to the Bugis, Indonesia’s famed shipbuilders, so your itinerary may include seeing giant wooden vessels being built on the beach.

A young girl looking out over a coastal village in Indonesia.

The Places in Between: Indonesia Positioning Cruises

A fun way to see Indonesia is to “position,” or cruise with the boat as it sails between these iconic regions. These trips are often longer in length and include more days at sea (sailing vs. venturing off the ship) but connect you to the unseen places of Indonesia and allow you to relax with the rhythm of the ocean. Positioning cruises are also excellent choices to add on to a voyage. For example, a three-week positioning itinerary could be to sail south from Sulawesi to Flores, then stay on the ship all the way west to Bali!

A coastal village built above the turquoise waters in Indonesia.

5. Know You Can Go Your Own Way – Indonesia Charters

Because ship sizes range on the smaller end (14 to 120 guests) for our Indonesia cruises, chartering your own vessel is a viable option for many groups and families. Talk to our experts to pursue a charter, which can equal per-cabin savings and more flexible routes so you can design your perfect itinerary.

A man looking out over the island at a small ship in Indonesia.

6. Let Us be Your Indonesia Cruise Guide

Most important when choosing your Indonesia ship and itinerary, speak with an experienced Indonesia cruise expert to get the full picture. This is a big trip, so make it the best it can be for your interests!  We are award-winning expedition cruise specialists with a focus on guided small group nature tours and custom travel.

Most important when choosing your Indonesia cruise, speak with an experienced Indonesia expert to get the full picture.

Our staff has decades of experience guiding and arranging expedition cruises and wilderness adventures. Our years of experience traveling in Indonesia can lend you the best insight for booking your trip.

A person paddle boarding along an island shoreline in Indonesia.  

In this Indonesia cruise guide, we’ve aimed to provide information to best inform your trip search, but since itineraries vary each year in this widespread region, we encourage you to contact us with any further questions on how to choose your Indonesia cruise.

The image of the boys in Papua New Guinea was taken by Adventure Specialist Andrew Browning.