Feeding preference of Macrochelys temminckii (Alligator Snapping Turtle) is not well known. Juveniles reared with no prior exposure to natural prey were tested for innate prey (i.e., fish) preference and foraging ability for mussels in coarse and fine substrates. Alligator Snapping Turtles consumed fish non-selectively, except that they selected Lepomis macrochirus (Bluegill) over Gambusia affinis (Mosquitofish) in live-prey trials, and Lepomis cyanellus (Green Sunfish) over Notemigonus crysoleucas (Golden Shiners) in carrion trials. Juvenile Alligator Snapping Turtles were less active and less successful when foraging for a benthic prey species, Lampsilis siliquoidea (Fatmucket), in coarse substrate than they were when the mussels were in fine and no substrates. Juvenile Alligator Snapping Turtle preference for Bluegill in a controlled environment corresponds to predator and prey habitat associations but could also be influenced by prey (i.e., fish) behavior. Likewise, enhanced activity and prey encounters in fine substrate are consistent with observations of Alligator Snapping Turtle habitat use.