How to Choose Your Indonesia Cruise

December 20, 2019 • Lis Larson

There are a variety of Indonesia cruise itineraries sure to captivate any traveler, but it can be hard to know where to begin when selecting your route and vessel. Our experts have scouted out the options and offer this comprehensive Indonesia cruise guide to walk you through your travel choices. Depending on your priorities, you can start at either the top or the bottom of this list to inform your trip search.

A female traveler in a green shirt standing on a wooden walkway on top of a steep grass covered hill surrounded by water.


You have questions.
We have answers.

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 cruise vibe to both luxury- and exploration-focused, 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.


See all the small ship options in Indonesia.

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.

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.

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 April through September.

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. 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.

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.
Photo by AdventureSmith Specialist Andrew Browning

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.

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 varied coastal geography.

The unique shape of the island into several long peninsulas offers coral reefs alongside varied 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.

Java & Sumatra Cruises

Most itineraries explore Indonesia from points north and east of Bali. However, select itineraries will cruise along the western Indonesian islands of Java and Sumatra, linking up with Singapore. While Java is home to a majority of the Indonesian population, small ship cruises here will opt to mostly visit uninhabited offshore isles and small villages. In this region travelers can explore unspoiled coral reefs, deserted black- and white-sand beaches, lush jungle and child volcanoes of the famous Krakatoa.

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!


See all the full list of itinerary options in Indonesia.

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

Because ship sizes range on the smaller end (12 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.

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! At AdventureSmith Explorations, 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 founder and president, Todd Smith, helped pioneer expedition cruising, and 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.

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.


You have questions.
We have answers.

This blog post on choosing your Indonesia cruise was originally published in May 2019 and has since been updated to reflect new itineraries and ships cruising in Indonesia. The most recent update occurred December 2019. For more articles, advice and inspiration visit our comprehensive small ship cruise guide.

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  • Hélène says:

    We are considering to go sailing in Indonesia either From 28-29 April or from 1 September. Visiting the spice islands, Flores or New Guinea has our interest. Definately do not want to go and visit Komodo; too much of a zoo we were told. Please advise me on your best and unique experience.

    Look forward to receiving your reply.

    Kind regards,
    Hélène Versluis

    • AdventureSmith Explorations says:

      Hi Helene,
      Thank you for your interest in small ship cruises in beautiful Indonesia. We offer a number of unique sailing itineraries to the Spice Islands and beyond; take a look at Sailing Indonesia: The Spice Islands, Sailing Indonesia: The Undiscovered Frontier and Spice Islands & Raja Ampat. All of which offer a number of alternative itineraries in this “off-the-beaten-track” area. One of our Indonesia specialists will be in touch with you soon to discuss the perfect trip.

  • kate collins says:

    We are two older ladies on a budget who would love to see the Spice Island any ideas would be welcome
    kind regards
    kate collins

    • AdventureSmith Explorations says:

      Hi Kate,
      The Spice Islands are an excellent choice for a remote, off-the-beaten-path adventure including culture, history and wildlife. We offer hand-picked Spice Islands options to cruise Indonesia. An Adventure Specialist will be in touch to help you find the right trip at the best price.

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