Raja Ampat Expedition: My 12-Day Sailing Itinerary from Ambon
Stories, Stops, and Surprises from Years at Sea
I’ve lost count of how many times I’ve cruised this route, from Ambon to Sorong, across the Banda Sea and through Raja Ampat but every single trip still manages to surprise me. The wildlife, the culture, the sheer variety of landscapes... it’s almost unfair how spoiled this part of the world is.
This isn’t your average holiday itinerary. it’s one I’ve fine-tuned over the years, filled with places I genuinely look forward to revisiting, where I’ve watched jaws drop and eyes light up. Whether you’re thinking about doing this trip yourself or you’re just daydreaming from your desk, here’s a peek into what a 12-day cruise through Indonesia’s forgotten isles and coral kingdoms really looks like.
Day 1: Ambon – Saparua – Nusa Laut
We usually board in Ambon, and after a round of welcome drinks and intros, I love easing into the journey with a visit to Saparua and Nusa Laut. These two islands are packed with charm, history, and the kind of reefs that make everyone dive in with zero hesitation.
Nusa Laut, in particular, always impresses, even those who’ve dived all over the world. The coral is pristine, and the water clarity is often crystal. Plus, the villages are spotless. I always say it’s the cleanest village in Maluku, and the locals take a lot of pride in that.
Day 2: Run & Ai – Small Islands with Big History
Most guests have never heard of Run or Ai, and that’s half the fun. These little Banda Islands were once so valuable (thanks to nutmeg) that the British literally traded Run for Manhattan. True story, 1667, Treaty of Breda.
Run is quiet, charming, and rich with nutmeg trees. Ai feels like a step back in time, with beautiful reefs just off shore. We snorkel, walk through spice plantations, and talk about how this tiny island changed the world. People are usually a little stunned by how much history is packed into a place so small.
Day 3: Banda Neira – Cloves, Cannons & Kora-Kora
Banda Neira is always a highlight. There’s something magical about arriving here by boat, volcano on one side, colonial buildings on the other. We usually visit Fort Belgica, stroll the town, and drop by a nutmeg processing house.
But the real adrenaline kick comes from riding in a Kora-Kora, a long traditional war canoe paddled in rhythm by a local crew. It’s loud, fast, and unforgettable. Every time we do it, people get off with the biggest grins on their faces.
Also, make sure to meet Maga, he’s a local champion who started a recycling initiative with village women, turning plastic waste into bags and baskets. A quiet revolution, island-style.
Day 4: Manawoka – The Lake Nobody Knows About
Most maps don’t even label Manawoka, but I make a point to stop here whenever I can. It’s tucked southeast of Seram and has this glass-clear blue lake that barely feels real. We anchor nearby, snorkel over bright, blooming coral gardens, and hop off the tender onto a stunning white sandbar that’s basically made for barefoot picnics and drone shots.
It’s peaceful, surreal, and always ends up being one of those “I had no idea this existed” moments for guests.
Day 5: Boo Island – Mantas & Karawapop’s Heart-Shaped Lagoon
Crossing into Raja Ampat, we reach Boo, a classic Misool favorite. There’s a famous site here where coral bommies are pierced with natural holes, everyone loves diving or snorkeling through them.
But what makes Boo extra special is the chance of seeing manta rays. They often swoop in, effortlessly elegant, and it never gets old. Honestly, the first time I saw one here, I squealed into my snorkel.
Then, we paddle into Karawapop, a lagoon shaped like a heart (yes, really). It’s gorgeous from the air and tranquil from the kayak. This spot is all about stillness and staring at your surroundings wondering how the heck it’s all real.
Day 6: Lenmakana Jellyfish Lake – Sunmalelen Cave – Andau
This day always feels like the weirdest and most wonderful part of the trip.
First, we hike up a steep path to reach Lenmakana Lake, where stingless golden jellyfish float in warm brackish water. I’ve swum here dozens of times and still find it surreal like being inside a snow globe of jellyfish.
Then we head to Sunmalelen Cave, with ancient hand stencils on the walls that pre-date pretty much everything. It’s humbling and a little eerie in the best way.
Day 7: Dayang – Yensawai Village Life
In the morning, we stop at Dayang for some fantastic snorkeling, great coral slopes, lots of fish, and often good visibility.
After that, we head to Yensawai, one of my favorite little villages in Raja Ampat. It’s great for a casual walk, meeting locals, and sometimes even getting invited into someone’s kitchen for snacks. If the group’s keen, we also offer an optional visit to a nearby mangrove waterfall. Totally worth it when you want a break from saltwater.
Day 8: Keruwo – Reef Drama Below the Surface
Keruwo is one of those underrated spots I always sneak into the itinerary. It’s got great diving, beautiful snorkeling, and vertical drop-offs that make the underwater world feel infinite. I’ve seen big schools of fish, curious turtles, and more than once, reef sharks cruising by calmly like neighborhood cats.
It's usually quiet here, and the reefs are in excellent condition. A great day for getting those “floating above paradise” shots.
Day 9: Melissa’s Garden – Piaynemo
I call this the “wow day.” First up: Melissa’s Garden, a dazzling coral garden filled with soft corals, damselfish, and the occasional passing turtle. It’s always a snorkel highlight.
Next is Piaynemo. Yes, the viewpoint with the million stairs. I warn guests, but they climb anyway, and once they see that sweeping view of limestone karsts dotting the turquoise water, it’s worth every step.
Day 10: Arborek – Cape Kri
Arborek is cheerful, colorful, and home to some of the warmest people I know. The village is small, with handwoven souvenirs and a house reef that always delivers.
Cape Kri, though? That’s where we go full National Geographic. It holds the world record for most fish species spotted in a single dive. We’re talking trevallies, barracudas, snappers, and sometimes a cruising shark. If there’s only one dive to do in Raja Ampat, this is probably it.
Day 11: Sapokren – Kalibiru
We start this day well before sunrise, hiking into the jungle near Sapokren to (hopefully) witness the Wilson’s bird of paradise performing his little dance. I’ve seen grown people cry watching it (read: me). It’s that special.
Later, we head to Kalibiru, a freshwater pool with insanely clear blue water and a tucked-away jump ledge. It’s quiet, shady, and the perfect place to soak in the last real swim before returning to civilization.
Day 12: Sorong – Back to Reality (With Better Stories)
And just like that, we’re back in Sorong. Disembarkation always feels bittersweet, no one’s ever quite ready to leave, and there are always a few people whispering about doing it again next year. (They usually do.)
What I Always Tell Guests to Pack:
Reef-safe sunscreen (please!)
Rash guards & swim leggings
A dry bag for wet tenders
Sarong (the MVP of island life)
A sense of humor and a big appetite for wonder
This itinerary has grown with me over the years. It’s not about hitting all the famous spots—it’s about rhythm, flow, and finding those special moments: a quiet snorkel in a secret bay, laughter over lunch on a sandbar, the gasps when a manta swoops by.
If you're considering doing this trip, all I can say is: go. And if you're already booked in, get ready. The ocean's waiting.
Thanks for reading and back to happily roaming!