Flights from the mainland arrive at two airports: Isla Baltra just north of Santa Cruz, and Isla San Cristóbal. There are almost an equal number of flights to Baltra and San Cristóbal.
The three airlines flying to the Galápagos Islands are Tame, Avianca and LAN. All operate two morning flights daily from Quito via Guayaquil to the Isla Baltra airport (two hours), which is just over an hour away from Puerto Ayora by public transportation. They also provide one or two daily morning flights to the San Cristóbal airport (1½ hours). Return flights are in the early afternoons of the same days.
Round-trip flights from Guayaquil start at $360, and round trips from Quito start around $440; the latter trips include a layover in Guayaquil, although you don’t have to get off the plane. It’s also possible to fly from Quito and return to Guayaquil or vice versa; it’s often more convenient to fly into Baltra and out of San Cristóbal (or vice versa). If you’re booked on a boat through an agency, it will likely make the arrangements for you. There is a limit of 20kg for checked luggage (per person) on the flight to the Galápagos.