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Choosing the Best Galapagos Itinerary

Punta Vicente Roca on Isabela Island in the Galapagos, Ecuador.

For many travelers, including us, a Galapagos Islands vacation is a once-in-a-lifetime experience. Here, naturalists have been observing curious animals for nearly two centuries. It was here that Charles Darwin proved evolution. And it is here that visitors travel to experience one of the world’s most remote and remarkable destinations. Yet every visitor to these enchanted islands faces the challenge of picking the best Galapagos itinerary.

Two small islands off the coast of Isabela Island in Elizabeth Bay. The best Galapagos travel advice we ever received is to carefully consider which Galapagos islands are best to visit, and then plan our Ecuador and Galapagos itinerary around that. And, from our perspective, Isabela Island is one of the best Galapagos Islands to visit.

Unless you have unlimited time and unlimited money, visitors have two options for Galapagos tours:

  1. Staying in a hotel on one of the islands and doing Galapagos day trips to sites on other islands. These Galapagos land tours can save you significant money, but you are much more limited in what you can see (primarily Santa Cruz Island from the Galapagos Islands resorts on the island).
  2. Or taking a luxury Galapagos cruise and staying on a live-aboard vessel for a number of days and traveling around to the various islands. This mobility gives you a chance to see the best Galapagos islands and not limit yourself to only one place.

From our perspective, sailing on a live-aboard boat is the best way to go for your Galapagos vacation. You’ll be able to experience these remarkable islands the way explorers have always experienced them – as sailors. Live-aboards also offer the ability to spend more time in different places – multiple shore landings or snorkels per day. (Note: We strongly recommend buying your own snorkel gear and taking it. While all Galapagos boats have equipment for you, there’s something about putting your mouth on a snorkel that hundreds of other people have used that we don’t love. We also found that some of the snorkel gear didn’t fit us properly. We wrote an in-depth guide about good snorkel gear here.)

The giant Galapagos tortoise on Isabela Island in the Galapagos Islands Ecuador.  Isabela Island is our vote for the best island in the Galapagos (the Islands west of Ecuador).  Not all of the Galapagos Island tours make it this far west, but you should try to get here, if possible.

The giant Galapagos tortoise

Itineraries are tightly controlled by the Ecuadorian government and the Galapagos National Park. The government permits landing parties in certain spots, vessels can only moor for the nights in certain locations and deviations can only be made under exceptional circumstances for safety reasons.

The government permits two general Galapagos itineraries, creatively called A & B by most operators (although some call their itineraries Galapagos Islands Northwest and Galapagos Islands Southeast, but the concept is generally the same).

Darwin Lake and Tagus Cove on Isabela Island in the Galapagos Islands, Ecuador.  If you are planning a trip to Galapagos Islands, this guide will help you choose the best itinerary for your needs.  And if you're wondering what to do in Galapagos, we've got ideas for that too.

Darwin Lake and Tagus Cove on Isabela Island

Why does any of this matter? The Galapagos Islands are not uniform. Each island is its own ecology due to the island’s geological formation. The Galapagos Islands stem from a hot spot deep in the earth.

As the Nazca Plate deep in the earth moves towards the South American Plate, thin spots or weak spots in the Nazca Plate allow lava to boil up to the surface. As the plate moves, various weak spots pop through the Nazca Plate resulting in the different islands.

From a geological standpoint, this means the eastern islands of the Galapagos are older than the western islands. And the eastern islands have had more time to develop vegetation. So the islands in the south and east are generally lusher and the islands in the north and west are rockier.

If you have two full weeks, most boats make both itineraries on alternating weeks, so you can see nearly all the islands. However, most visitors are only able to spend one full week for their Galapagos trip, so they need to choose between the two itineraries.

A male Magnificent Frigatebird further to the east in the Galapagos, where vegetation is more plentiful.  Bird watching is certainly one of the best things to do in Galapagos trips.

A male Magnificent Frigatebird further to the east in the Galapagos, where vegetation is more plentiful

Galapagos Islands Itinerary A

The eastern Galapagos itinerary generally visits:

  • Baltra Island – This is the location of a small harbor and the Galapagos international airport (while there is another airport in the islands, most flights to Galapagos land here). It is a former military base and some of the old base can still be seen.
  • Santa Cruz Island – This is the main island of the Galapagos, home to the town of Puerto Ayora and also the Charles Darwin Research Station and the forest highlands.
  • Floreana Island – Common sites to visit are Punta Cormorant, the Post Office Bay and the Devil’s Crown.
  • Espanola Island – Sites of Gardner Bay and Punta Suarez.
  • San Cristobal – This island has a large number of sites, including Puerto Baquerizo Moreno, the San Cristobal Interpretation Center, Punta Pitt, and the stunning Leon Dormido rock.
  • Santa Fe – Some itineraries can also include the small Santa Fe Island.
Lava cactus growing out of cracks in the flow on Fernandina Island in the Galapagos at Punta Espinoza.  The best way to visit Galapagos Islands is on a small cruise boat, but there are Galapagos alternative trip ideas that are land based, but they won't get you to remote islands like Fernandina Island.

Lava cactus growing out of cracks in the flow on Fernandina Island

Galapagos Islands Itinerary B

The western Galapagos Islands itinerary generally visits:

  • Baltra Island – This is the location of a small harbor and the Galapagos airport. It is a former military base and some of the old base can still be seen.
  • Santa Cruz Island – This is the main island of the Galapagos, home to the town of Puerto Ayora and also the Charles Darwin Research Station and the forest highlands.
  • Genovesa Island – Genovesa (or Tower Island) is a rocky volcanic caldera that is actually due north of Santa Cruz and home to Darwin Bay and the Prince Phillips Steps.
  • Santiago Island – The stop here usually take in vast James Bay.
  • Isabela Island – This is the largest island in the Galapagos and most western Galapagos itineraries feature many stops, including Elizabeth Bay, Punta Vicente Roca, Urbina Bay, Tagus Cove and the massive Sierra Negra volcano caldera. This is our vote for the best island in the Galapagos.
  • Fernandina Island – This is a chance to see the lava fields of Puna Espinoza.
One of the highlights of the western Galapagos itinerary is the lava flow at Punta Espinoza on Fernandina Island.  If you're wondering which Galapagos Islands to visit, this would be a good choice!  The island is popular with Galapagos cruise boats with companies like Ecoventura or Linblad Galapagos Expeditions.

The lava flow at Punta Espinoza on Fernandina Island.

Which Galapagos Itinerary is Best?

Ideally, visitors would take in two full weeks and do both itineraries. However, for many travelers, that’s not realistic. And it wasn’t possible for us.

We only had two weeks for this trip – one week on the mainland of Ecuador exploring the mountains and one week in the islands of the Galapagos (however, the different climates presented some packing challenges, so be sure to check What to Pack For Ecuador and the Galapagos).

For us, we wanted to see the other-worldly lava landscapes so we chose the western Galapagos trip. However, there’s really no bad choice! The best Galapagos cruise itinerary is the one that takes your interests into account.

No matter which itinerary you select for your Galapagos Islands tours, you'll have amazing wildlife encounters like this mother and baby sea lion (the Spring is the best time to visit Galapagos to see babies). Photographing the wildlife was one of the best things to do in the Galapagos Islands for us!

No matter where you go, you’ll have amazing wildlife encounters like this mother and baby sea lion

The Best Galapagos Islands to Visit

If you don’t have two weeks to visit all of the islands and your trying to prioritize your Galapagos Island vacation, here are some things to consider. No since one week itinerary will hit all of the hightlights. You will have to make some choices.

For us the best Galapagos Islands are historic Floreana Island (home of Post Office Bay) and San Cristobal Island with its numerous sites and the incredibly beautiful Leon Dormido rock formation. These are included on the Galapagos Itinerary A (or the southeast).

From the Galapagos Itinerary B (or the northwest), the best islands are Genovesa Island or Tower Island, with its rocky caldera and the chance to snorkel with dolphins in the wild. Also a highlight are the rocky lava fields of Fernandina Island and the numerous sites of Isabela Island (including Punta Vicente Roca with its cave and snorkeling with turtles). If you can’t tell, we’re slightly biased to this Galapagos Islands tour option.

And both itineraries include the chance to what life is like for the people of Ecuador in Puerto Ayora on Santa Cruz Island.

The Sierra Negra Isabela volcano caldera in the Galapagos Islands.  While most people visit the islands on a cruise, this volcano is also accessible to people on Galapagos land based tours.

The Best Time to Visit the Galapagos Islands

There is really no bad time for your Galapagos tour, but it does come down to what you really want to see. There are only two seasons in the Galapagos Islands: cool and dry (generally early-June through November) and warm and wet (generally early-December through late-May). Each season has its benefits.

Cool and Dry Season in the Galapagos Islands

The cooler and drier season last from early-June through the month of November. During this time, nutrient rich waters bring an abundant of marine life close to the islands. If you’re a scuba diver, this is prime Galapagos diving season. On land, the birds are aggressively hunting fish in the water and getting ready for baby season.

The downside here is that the seas can be quite a bit rougher. If you are planning a cruise in the Galapagos and have motion sickness, you may have some problems.

Warm and Wet Season in the Galapagos Islands

Many of the best Galapagos tours focus on the spring: the warm, wet season. This generally lasts from early-December through late-May). During this time, there’s a daily rain drizzle that springs the islands with water. We should note that we were in the Galapagos in March and only experienced this about half the time.

The warm and wet season brings with it babies…when you can find them. Green sea turtles lay their eggs in December and January and you’ll find lots of evidence of turtle nests on the beaches.

The downside to the warm and wet season is that it can sometimes be hot – really hot. The Galapagos Islands sit at the Equator, so the sun can be really intense. This isn’t tanning at the beach sun. It is cover yourself or burn to a crisp sun.


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What do you think about Choosing the Best Galapagos Itinerary?

  1. Shannony September 19, 2015 at 12:50 pm #

    Hey – wow… awesome photos! We just got back from a trip to the Galapagos and did a 5 day catamaran tour that pretty much followed the “A” itinerary you mentioned. It was pretty awesome and I’m all for the live on boat experience. Pretty sure our trip would have suffered with day trips alone and we wouldn’t have been able to see nearly as much.

    Love those sea lions! 🙂

    • Cassandra Fairchild June 12, 2019 at 7:54 pm #

      May I ask which catamaran tour you used? Did you book beforehand?

      • Lance Longwell June 15, 2019 at 8:30 pm #

        We did not go on a catamaran. We went on a mono-hull sailboat (the Beagle). We prebooked our trip, however, we have had friends who have good luck with last minute Galapagos trips.

  2. Samantha December 5, 2015 at 10:24 am #

    I’m starting to plan a Galapagos trip for probably 2017 but didn’t know there were two different itineraries for the islands so this is super helpful. I guess I’ll just need to set aside at least 2 weeks so I can do both! The Galapagos is one of my dream destinations so I want to explore as much as possible.

    • Lance Longwell December 5, 2015 at 12:31 pm #

      Samantha, if time is no limit, do it. Regrettably, we only had one week in the Islands. That meant we missed Post Office Bay and some of the other sites that we’d read about. I guess it just means we’ll have to back again!

  3. fadiyah March 5, 2016 at 4:17 am #

    Darwin Lake my dream destination,, what a beautiful view <3 Love it

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