San Cristobal and Baltra (which serves Santa Cruz) have airports for flights from the mainland. Isabela has a landing strip for local island-hopper flights.
Currently, 3 operators provide flights to Galapagos:
Tame (pronounced “Tamay”)
Avianca (formerly Aerogal)
There are daily flights, from Quito and Guayaquil, to San Cristobal and Baltra . Most flights from Quito pass through Guyaquil en route to and from the islands. Flights leave in the morning, arriving between 10:00am and 12:30pm, and return in the afternoon, arriving between 3:00 and 5:30pm.
The flight from Guayaquil to Galapagos, takes about 1 hour, 40 minutes. From Quito via Guayaquil takes about 3 hours, 10 minutes.
Flights from Guayaquil are around $50 less than from Quito but the cost is the same whether flying to San Cristobal or Baltra (Santa Cruz).
To San Cristobal or Baltra?
You can fly from the continent to either San Cristobal or Baltra.
If you are going on a cruise, you may be embarking and disembarking at:
Puerto Baquerizo Moreno, San Cristobal
Puerto Ayora, Santa Cruz or
Some cruises start at one port and conclude at another.
If you are taking day-trips to uninhabited islands such as Bartolome, Plazas, N Seymour and others, you will be leaving from Puerto Ayora or Baltra.
If you are island hopping among the inhabited islands then could could start in any of the above.
There is good diving off Santa Cruz and San Cristobal but the live-aboard dive boats operate out of San Cristobal.
San Cristobal is the hot-spot for surfing, drawing enthusiasts from all parts of the world.
Finally: if you are going fishing then you definitely want to be in San Cristobal.
To San Cristobal
Puerto Baquerizo Moreno (San Cristobal) is more laid-back, and less commercial than Puerto Ayora (Santa Cruz). Although it cannot match Puerto Ayora’s fine hotels, restaurants and galleries, neither does it match their high prices.
San Cristobal does have some good restaurants and reasonable hotels, as well as some excellent B&B’s and generally offers much better value. It is also less polluted and the shoreline is accessible to the public and visible from many parts of town.
Though long over-shadowed by Santa Cruz, San Cristobal is rapidly gaining in popularity.
To Baltra (for Santa Cruz)
Santa Cruz’s central location in the archipelago has led to it becoming the main hub for tourism in the Galapagos.
Puerto Ayora boasts many fine hotels, restaurants and galleries. It is considerably more developed, crowded and commercial than San Cristobal. There is very limited access to the waterfront which, in any event, is rather polluted.
Baltra (Santa Cruz) was the first airport so flight information calls and screens refer to Baltra as "Galapagos" or "Galapagos Islands" (airport code: GPS). Flights to San Cristobal refer specifically to "San Cristobal" (airport code: SCY).
Through Quito or Guayaquil?
Although there are some international flights arriving early enough or leaving late enough, the chances are you will need to spend a night in either Quito or Guayaquil. Each route has its pro’s and con’s.
No visit to Ecuador is complete without a visit to the historic centre of Quito and the immediate region has numerous attractions, including Mitad del Mundo (equator park) the Mindo Cloud Forest, Otovallo, the rooftop train ride to Rio Bamba to name just a few.
Quito is right on the equator but at 2,800m (9,200ft) above sea level the climate is mild. The elevation may be a concern for those prone to acute altitude sickness.
Quito is now served by a new airport which has been built some 20 kms outside the city. Until recently, before they completed the connecting highway, it could take 2 to 3 hours to get downtown from the airport. Now it should only take half that time.
You can a taxi downtown for $35 to $50 or take the “Airport Express” bus, which runs every ½ hour between the old and new airports. It’s a modern, comfortable bus and costs $8.00. If you are there in daylight you can enjoy some spectacular scenery along the way.
While it has fewer attractions and is less safe than Quito, Guayaquil is significantly more convenient for those travelling directly to Galapagos.
Most hotels are only minutes away from the airport, which is regarded as one of the best in South America.
As Galapagos flights travel through Guayaquil en route to and from Quito, it means that you leave a little later in the morning and get back a little earlier in the afternoon.