Paul Schicke
Written by Paul Schicke Senior Expedition Designer

Updated: January 22, 2024
Published: December 18, 2023


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Galapagos Blue-footed Booby

A Galapagos cruise provides an exotic escape from the mundane across the world’s most diverse island chain while catering to your every whim. However, the logistics of boarding your vessel can seem confusing because a cruise through the Galapagos Islands has several differences from many popular cruising destinations around the world. While the voyage through the islands is out of your hands and part of a predetermined cruise itinerary, depending on which cruise company you book with some cruise passengers will need to book their own transportation from the mainland to their departure port in the Galapagos.

If tackling travel arrangements to begin your Galapagos cruise feels stressful, consider a cruise package that includes air travel. All-inclusive bundles will eliminate the stress of planning your trip and let you simply enjoy the ride. Even if your itinerary doesn’t come with prepaid plane tickets, a helpful cruise company or travel agency will help you navigate to and from your cruise.

With those options in mind, let’s explore the primary ports that could be the launchpad for your Galapagos Islands luxury cruise.

The Basics: 2 Very Important Pieces of Information to Consider

1. All Galapagos Cruises Start and End in the Galapagos Islands

The first thing to know is that, regardless of the ship or cruise company you book with, all Galapagos cruises begin and end in the Galapagos Islands. There are no Galapagos cruises that depart from any port within mainland Ecuador (or from anywhere else in South America). In order to embark on any Galapagos cruise, you must first make your way to the islands from the mainland, and the only way to get to the Galapagos is by air. Read a detailed step by step guide on how to get to the Galapagos.

2. Don’t Book Your Galapagos Flights Before You Have Booked Your Cruise

One of the most common mistakes travelers make when visiting the Galapagos is to book their flights to and from the islands before they have secured all their cruise plans. It can be tempting to do so when airlines offer attractive Galapagos flight specials. However, this is a BIG mistake. We’ve experienced this with several travelers who bought Galapagos air tickets in advance only to discover that either all cruises were sold out for their dates or the flights they purchased didn’t match up with available cruise departure dates. Or how about learning that you booked flights into or out of the wrong Galapagos airport based on your cruise itinerary? All the above can result in travelers having to change flights and pay more than they would have simply by deciding what Galapagos cruise they want to book before purchasing flights.

Onboard view from the Galapagos Grace Yacht

Galapagos Cruise Origin Ports

Embarking on your Galapagos adventure directly from the archipelago is the only way to do a Galapagos cruise. And Galapagos cruises can begin or end in one of 3 places: Baltra Island, Puerto Ayora (on Santa Cruz Island) and San Cristobal Island.

Baltra Island:

Baltra Island is home to the Galapagos’ busiest airport, with the official name of Seymour Galapagos Ecological Airport (airport code GPS). This airport receives inbound flights from both Quito and Guayaquil, and is the access point for most Galapagos Islands cruises. Most ships and yachts in the Galapagos will depart directly from Baltra Island, requiring you to take a 5-minute bus ride from the airport to the main bay on the Islands where passengers board their zodiacs on the main dock to go to their ships anchored in the bay.

Luggage at the Baltra Island Airport

Puerto Ayora on Santa Cruz Island

Puerto Ayora is the main port town of the Galapagos, and is located on Santa Cruz Island. Several cruise companies also have itineraries that either start or end in Puerto Ayora. To get to Puerto Ayora, passengers also need to fly into Baltra Island Airport (GPS). From the airport you take a 5-minute bus ride to the Itabaca channel crossing, where a brief ferry ride will transport you across the channel to the Islands of Santa Cruz. On the other side you will then need to take a bus or a private taxi to the port town of Puerto Ayora, which is about an hour away via a paved road.

Once you reach the town of Puerto Ayora, you will head to the main municipal dock where a zodiac from your selected cruise ship will pick you up to take you onboard.

Puerto Ayora Galapagos Islands
© A Flores López

Puerto Baquerizo Moreno on San Cristobal Island

The third and final cruise origin point in the Galapagos is the port town of Puerto Baquerizo Moreno, nestled on the southwestern coast of San Cristobal Island. To get here you must take an inbound flight from either Quito or Guayaquil in mainland Ecuador to the San Cristobal Galapagos Airport (airport code SCY). This airport provides a frequent entry and exit point for tourists, whose cruises begin or end in the island of San Cristobal.

Puerto Baquerizo Moreno on San Cristobal Island
© Iris Diensthuber

Make Sure You Are Flying In and Out Of to the Correct Island in the Galapagos

The majority of 6, 8, and 15-day Galapagos cruises begin and end in different Islands within the Galapagos. This means that your inbound and outbound Galapagos flights need to be to/from different airports. The good news is that, because this is very common for most Galapagos cruise companies, the airlines that fly to the Galapagos (Avianca and Latam) don’t generally charge you more for flying in and out of different Galapagos airports. However, if your cruise itinerary requires you to fly in and out of different airports, you may have to call the airline or a travel agency to book your flights over the phone as multi-destination routes are not always an option when booking online.

Airplane overhead view into the Galapagos

Plan for Smooth Sailing on a Galapagos Cruise

No matter where you embark, the Galapagos Islands will show you the most majestic and mysterious sights in the world. However, as we have explained above, getting the airports and Islands right based on your selected cruise itinerary is a crucial first step.

As you map out your plans for a Galapagos cruise, know that each route holds the promise of a once-in-a-lifetime adventure like no other. If you have any questions or concerns, feel free to book a call with one of our Galapagos Expedition Designers.

Galapagos Sea Lion with Evolution yacht sunset
Paul Schicke
By Paul Schicke
Senior Expedition Designer

Hello! My name is Paul. I am a photographer, traveler, teacher and writer. I have extensive experience in travel to Galapagos, Peru, Patagonia and the western seaboard of South America specializing in ways travelers can experience these once-in-a-life destinations like locals on the road. Lover of wine, chocolate, travel, coffee, and helping others plan vacations of a lifetime!

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