Emetebe and Fly Galápagos connect Isabela to San Cristóbal and Baltra. One-way flights cost $175. You must pay a $10 fee on arrival at the airport in Puerto Villamil.
There are daily 6am/3pm boats to Santa Cruz ($30, 2¼ hours) from Puerto Villamil. From Santa Cruz, boats leave at 7am/2pm. Tickets can be purchased at the dock or from Transmartisa, near the main plaza. When arriving at the passenger pier east of town you have to pay a $5 fee.