First you must fly into contiental Ecuador to either Quito or Guayaquil; There are several commercial flights arriving into Ecuador everyday.
The most efficient way to get to the Galapagos from mainlaind Ecuador is by air. Your Galapagos flight booking is guaranteed with your cruise confirmation. All international connections are from mainland Ecuador . There are flights from Quito with a stop over in Guayaquil, and from Guayaquil to Baltra or San Cristobal where your cruise will begin. Your flight will take 30 minutes to get from Quito to Guayaquil and about one and a half hours from Guayaquil to Galápagos - Baltra or San Cristobal .
The airlines have established low and high season for the flights, and these are:
High Season: Nov 01 - Apr 30 + Jun 15 - Sep 14
Low Season: May 01 - Jun 14 + Sep 15 - Oct 31