How to Get from San Cristobal to Isabela Island: Why We Flew

Route: San Cristobal (SCY) to Isabela Island (IBB)

Airline: Emetebe Airlines

Flight time: 43 minutes

Departure: 8:00 am daily

Cost: approximately $200 per person for the flex plus fare (35 lbs included)

Aircraft: Britten Norman BN 2-A, seats 6 passengers plus pilot

There is a ferry alternative, but it requires a stop in Santa Cruz and can take up to 10 hours total. For most travelers doing a land-based island-hopping itinerary, the flight is the obvious choice.

The ferry network in the Galapagos connects Santa Cruz to San Cristobal and Isabela to Santa Cruz (which we did!), but not San Cristobal directly to Isabela.

There is no direct route between these two islands. You must stop in Santa Cruz and board a new boat.

Here is what that actually looks like in practice.

The ferry from San Cristobal to Santa Cruz departs at 7:00 AM and takes 2 to 2.5 hours. You then arrive in Puerto Ayora, wait for the afternoon departure, and board the 3:00 PM ferry from Santa Cruz to Isabela, another 2 to 2.5 hours.

Add an hour of required early arrival at each pier, water taxi transfers on both ends, and you are looking at a full day of transit, easily 10 hours door to door.

The Emetebe flight takes 43 minutes. We did the math quickly and booked the flight.

For a full breakdown of all inter-island ferry and flight options including which route to take and when, read my Ferry or Flight Between Galapagos Islands guide.

Two airlines operate inter-island flights in the Galapagos. After doing my research, Emetebe was the clear choice for us.

Emetebe has been operating since 1993, over 30 years of flying the Galapagos archipelago. That kind of experience and track record in a remote environment was exactly what we were looking for.

I also reached out to their team via email before the trip with a question about flight numbers.

Victor Duque responded quickly and helpfully, explaining that flight numbers 101, 201, and 301 departing at the same time are simply different tail numbers on the same route with identical service.

That kind of responsive customer service from a small regional airline told me a lot about how they operate.

For us, experience and communication were the deciding factors. Emetebe delivered on both.

Full disclosure: I am not a small plane person. I white-knuckle bush planes in Tanzania and seaplanes in the Maldives. The Emetebe flight is smaller than both of those!

The aircraft is a Britten Norman BN 2-A, six passengers in rows of two, no co-pilot. My husband and I were in Row 1.

I could have tapped the pilot on the shoulder without leaning forward. The air vents kick on once you are airborne, which helps.

And despite my nerves, the 49-minute crossing was genuinely smooth. One of my better small plane experiences, honestly.

One more thing worth knowing: you can apparently pay extra to sit in the co-pilot seat!

This is the section that requires the most attention.

Emetebe’s baggage policy is strict and the weight limits are genuinely tight, especially if you are traveling with snorkel gear (like us, see my photo above with all of my personal gear at Concha de Perla!), a camera, and anything resembling a normal wardrobe for two weeks.

The basics:

• Fares come with a baggage allowance ranging from 15 lbs to 35 lbs per person, covering both checked luggage AND carry-on combined
• We purchased the Fare Flex Plus at approximately $200 per person, which includes 35 lbs
• We then each purchased an additional 25 lbs at $1.50 per pound, adding $37.50 per person
• Total per person: approximately $237.50

Buying extra weight: If you need more than your included allowance, buy it online more than 24 hours before your flight at $1.50 per pound. Wait until within 24 hours and the rate jumps to $2.00 per pound. Buy early.

One more thing about weight: Each passenger’s luggage is weighed individually. If you and your travel partner are under the same reservation, you cannot combine allowances. If one person is over and the other is under, you cannot transfer the difference.

Your bags might not make it on the same flight: Due to payload restrictions, your checked bags occasionally travel on a later flight. Your bags will be held securely and can be collected at the Emetebe office on the island.

The Emetebe office opens at 6:45 AM and not a minute before.

We arrived at 6:25 AM and were the first ones there. Learn from us: there is no benefit to arriving before it opens.

After checking in at the office, do not sit down and wait there.

Walk out, turn left, and head to the main airport terminal. That is where you wait.

When Emetebe is ready, they call passengers from the main terminal to go through security. After security, you wait briefly before heading to the plane.

By the way, there is a lounge worth knowing about.

The San Cristobal airport lounge: If you have Priority Pass access, the lounge is genuinely nice. Modern, clean, excellent air conditioning, and a very nice bathroom. We used ours through our Chase card.

The lounge provided a little box with a ham and cheese sandwich, chips, and an apple. Water, tea, or coffee was offered. For a short pre-flight wait, a lovely touch.

The luggage inspection: At some point before boarding, your bags may be called for inspection.

Do not panic.

This is standard and routine, checking for fruits, plants, and anything that could disrupt the Galapagos ecosystem. It happened to us (my makeup bag flagged their system somehow) and was completely uneventful.

We departed at 8:19 AM and were in flight by 8:26 AM.

Total flight time: 43 minutes.

The pilot ran through the full pre-flight checklist. Then he taxied all the way to the end of the runway, turned around, and took off. The whole sequence was deliberate and professional.

From Row 1 I could see essentially everything happening up front. No partition, no curtain, no distance between us and the cockpit. The air vents came on once we were airborne, and the flight was smooth and uneventful.

We landed at Isabela at 9:09 AM and were in a taxi (arranged by our hotel) to the Cormorant Beach House within minutes.

We arrived before 9:30 AM with a full day on Isabela ahead of us. That is the difference a morning flight makes!

Here is something worth building your whole trip around. The Emetebe flight from San Cristobal to Isabela departs at 8:00 AM.

The reverse, Isabela to San Cristobal, departs at 2:00 PM.

That afternoon departure on the return route effectively eats half a day on a beautiful island while you sit around waiting.

We structured our trip as San Cristobal to Isabela to Santa Cruz, which meant morning arrivals on each new island with almost a full day ahead of us every time.

Morning flights also tend to be smoother since winds pick up as the day heats up. One more reason to book early departures.

✔️  Book Emetebe for its 30-year track record flying the Galapagos.

✔️  Structure your route as San Cristobal to Isabela to Santa Cruz for morning arrivals throughout.

✔️  Buy extra weight more than 24 hours before departure at $1.50 per pound.

✔️  Weigh every item including carry-on, camera, purse, and laptop before the counter.

✔️  Allowances do not transfer between passengers on the same reservation.

✔️  Arrive at 6:45 AM when the office opens. Not before.

✔️  After checking in, go to the main terminal to wait. Not the Emetebe office.

✔️  Luggage inspection is routine. Do not stress if your bags are called.

✔️  Pack essentials in one identifiable bag in case of a payload delay on a second bag.

If you end your island-hopping on Santa Cruz before flying home from Baltra, you will have already cleared the Emetebe flight and its strict weight limits before doing your souvenir shopping.

We did most of our shopping in Puerto Ayora on Santa Cruz: 26 Chocolápagos chocolate turtles in every flavor imaginable (we gambled on them surviving the journey home without becoming turtle soup, and they mostly did, though a couple of little heads did not make it) plus a stunning crystalline blue-footed booby ceramic mug from Opuntia.

Then we grabbed two t-shirts at Garua at Baltra Airport on the way out.

Had we still been flying Emetebe with 60 lbs of luggage already accounted for, that shopping would have felt considerably more stressful.

End on Santa Cruz. Shop freely. Fly home happy.

I spent more time researching this flight than it actually took to fly it.

The Emetebe experience was smooth, efficient, and genuinely enjoyable in a way I did not expect from a six-seat plane over the Pacific.

The baggage rules take some planning but nothing that a good packing list and an early weigh-in cannot solve. And arriving on Isabela before 9:30 AM with the whole island ahead of us made every bit of that planning worth it.

Would I fly Emetebe again? Without a second thought!

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Questions about our experience flying to Isabela from San Cristobal on Emetebe? 

Let me know in the comments below!