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.
Note: This information was accurate when it was published, but can change without notice. Please be sure to confirm all rates and details directly with the companies in question before planning your trip.