The restaurants at the Royal Palm Hotel and Finch Bay Hotel are both excellent. If you're not staying at either of these, you might consider a splurge and dine at one or both while in Puerto Ayora. In both cases, reservations are essential, and the food will be quite a bit more expensive than anything else you'll find around town.
For pizzas, fresh seafood, hearty breakfasts, and a range of international dishes, you can head to Café Hernan (tel. 05/2526-573; Av. Baltra and Av. Charles Darwin), which has a pretty open-air dining room and laid-back vibe. The Rock (tel. 05/2527-505; Av. Charles Darwin) is a popular local joint, with large picture windows fronting the busy main street through town.