Ferry or Flight Between Galapagos Islands? A Complete Guide
One of the most common questions I see in Galapagos planning groups is some version of this: should I take the ferry or fly between islands?
The honest answer is: it depends on which route you are doing and what time of year you are going. After 17 days island hopping with my husband between San Cristobal, Isabela, and Santa Cruz, here is the clearest breakdown I can give you.
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Quick Answer: Three Routes at a Glance
Ferry vs. plane routes in the Galapagos
There are three inhabited islands most land-based travelers visit: San Cristobal, Isabela, and Santa Cruz.
The inter-island transportation options are not the same for every route, and the right choice for one leg of your trip may be the wrong choice for another.
Transportation options for interisland travel in Galapagos
Route 1: San Cristobal ↔ Isabela
Flying with Emetebe from San Cristobal to Isabela
The answer: fly. Every time.
There is no direct ferry between San Cristobal and Isabela.
The only ferry option requires stopping in Santa Cruz, which turns a short journey into an all-day ordeal.
You are looking at a 2-hour crossing to Santa Cruz, a wait, then another 2-hour crossing to Isabela, plus water taxi transfers on both ends.
The Emetebe flight takes 45 minutes.
For everything you need to know about the flight including baggage rules, what the tiny plane is actually like, and why we chose Emetebe Airlines, read my San Cristobal to Isabela flight guide.
Quick facts: San Cristobal ↔ Isabela flight
- Airline: Emetebe
- Departure: 8 am daily (San Cristobal to Isabela) and 2 pm daily (Isabela to San Cristobal)
- Flight time: 45 minutes
- Cost: approximately $157 to $192 per person depending on fare and luggage
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Route 2: Isabela ↔ Santa Cruz
Queen Arlett Ferry in Santa Cruz
The answer: depends on the time of year.
This is the route where the ferry genuinely makes sense in the right conditions.
Unlike the San Cristobal to Isabela leg, there IS a direct ferry between Isabela and Santa Cruz and it drops you right at the Puerto Ayora pier (which is the heart of Santa Cruz!).
No transfers, no buses, no Baltra logistics. You step off the boat and your hotel is a short walk away.
We took the 6 am Queen Arlett ferry in mid-May and arrived in downtown Santa Cruz at 8:05 am.
The Emetebe flight on the same route departs at 9:00 am, lands on Baltra around 9:30 am, and after the bus, water taxi, and 40-minute taxi into town, the earliest you are at your hotel is around 11:00 am. Three full hours later, and more expensive.
For the complete ferry experience including the early morning logistics, seasickness tips, and exactly what to expect at the pier, read my Queen Arlett ferry review.
When to take the ferry to and from Santa Cruz and Isabela
Quick facts: Isabela ↔ Santa Cruz ferry
- Ferry: Queen Arlett (newest and largest option at the pier)
- Departure: 6 am and 3 pm daily (Isabela to Santa Cruz) and 7 am and 3 pm daily (Santa Cruz to Isabela) * Queen Arlett only operates at 6 am from Isabela and 3 pm from Santa Cruz
- Crossing time: just over 2 hours
- Cost: $35 per person
- Arrives: Puerto Ayora pier in downtown Santa Cruz on Isabela → Santa Cruz route
Quick facts: Isabela ↔ Santa Cruz flight
- Airline: Emetebe
- Departure: 9 am daily (Isabela to Santa Cruz) and 1 pm daily (Santa Cruz to Isabela)
- Flight time: 30 minutes (plus 1.5 hours of transfers from Baltra)
- Cost: approximately $157 to $192 per person depending on the fare and luggage
- Arrives: Baltra Island (requires transfers to reach Puerto Ayora) on Isabela → Santa Cruz route
Route 3: San Cristobal ↔ Santa Cruz
Emetebe plane
The answer: fly.
I did not personally do this route so I want to be upfront about that.
But the research is consistent and experienced Galapagos travelers are largely in agreement: fly this one.
Ferries do run between San Cristobal and Santa Cruz twice daily at $35 per person, taking approximately 2 hours. But this crossing has a reputation for being rougher and less comfortable than the Isabela to Santa Cruz route.
That said, if you do decide to ferry this route, the one ferry worth looking at is the Gaviota. They only operate this specific route:
- San Cristobal → Santa Cruz at 7:00 am
- Santa Cruz → San Cristobal at 3:00 pm.
I actually reached out to them directly during our planning (mistakenly thinking they did the Isabela → Santa Cruz route) and their WhatsApp communication was fantastic. Super kind and responsive.
The boat holds 38 passengers in a 2×2 forward-facing recliner seat configuration, which from the outside looks very similar to the Queen Arlett.
If you are on a strict budget and traveling in the calmer season, the ferry is an option. Just go in with realistic expectations about the crossing conditions.
Quick facts: San Cristobal ↔ Santa Cruz ferry
- Departures: 7 am and 3 pm daily
- Crossing time: approximately 2 hours
- Cost: $35 per person
Quick facts: San Cristobal ↔ Santa Cruz flight
- Airline: Emetebe
- Departure: 8 am daily (San Cristobal to Santa Cruz) and 1 pm daily (Santa Cruz to San Cristobal)
- Flight time: 1 hour 30 minutes (via Isabela)
- Cost: approximately $203 to $238 per person depending on fare and luggage
The Seasickness Question
What we did to prevent seasickness on Queen Arlett ferry from Isabela to Santa Cruz
This applies to any ferry crossing in the Galapagos.
My husband is prone to seasickness and it was one of our biggest considerations when planning.
His system that worked:
- EmeTerm seasickness band (the kind that sends mild pulses to the median nerve)
- Bonine taken 1 hour before boarding
- Ginger chews throughout the crossing.
A few other practical tips:
- Sit toward the back of the ferry for better airflow.
- Forward-facing seats are better than side-facing benches (choose your ferry wisely!)
- Have medication ready before you board, not after nausea starts.
- Always carry a small trash bag in your backpack on any ferry. Just in case.
The Itinerary Order That Maximizes Your Time
My recommended Galapagos itinerary order
The direction you island hop affects how much time you actually get on each island.
We did San Cristobal to Isabela to Santa Cruz, which meant morning arrivals every time. Go the other direction, and you arrive on the islands in the afternoon.
That is half a day gone.
My recommended order: San Cristobal first, then Isabela, then Santa Cruz.
An added bonus: if you end on Santa Cruz, you will have already cleared the Emetebe flight and its strict baggage limits before doing your souvenir shopping in Puerto Ayora and at Baltra Airport on the way out.
Final Thoughts
Three routes. Three different answers.
The confusion comes from treating every crossing as the same decision. They are not.
San Cristobal → Isabela: FLY.
Isabela → Santa Cruz: FERRY in calm season, FLY in the rough season.
San Cristobal → Santa Cruz: FLY.
Know your route, book early, and you will spend far more time actually on the islands than getting between them. That is the whole point of being there.
I’m Nichole, the author of all the blog posts on Enriching Pursuits. Think of me as your geeky discerning travel friend who dives deep (Google Page 20, forums, travel groups deep!) to uncover the best ways to enjoy exceptional outdoor adventures and foodie experiences.
My husband and I are experienced snorkelers, day hikers, and casual cyclists who also love delicious street food, an incredible glass of wine, and the occasional Michelin-starred meal.
Balancing full-time careers, we cherish every second of our vacation days and love sharing tips to help you do the same. If this sounds like your kind of travel, subscribe below or drop me a note with any questions. I’d love to hear from you!
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