The Island Fish Company is located on the Gulf side and has a direcrt via overlooking Gulfpointe. It includes indoor & outdoor dining, a full menu and amazing Margaritas.
On the south end of Marathon, Porky's serves fantastic Bar-B-Q. They have an extended menu with something for everyone in the family as well as a full bar.
You can't say enough about the Wooden Spoon. A classic "greasy spoon diner", it serves the best breakfast in all the Florida Keys. Go early, the lines build quickly.
Sparky's Landing is located on the canal in Key Colony. Reachable by boat or car, you can dine inside or out. It has great food, friendly service, and a full bar.