This study addresses habitat differences of two sympatric turtle species, alligator snapping turtles (Macrochelys temminckii) and eastern snapping turtles (Chelydra serpentina) in six watersheds in southeastern Missouri. We found that alligator snapping turtle presence corresponded with higher abundance of submerged physical structures in the stream, deeper water, relatively higher levels of detritus, and warmer water temperatures. Greater amount of aquatic vegetation was important in characterizing eastern snapping turtle presence in traps. Eastern snapping turtles and alligator snapping turtles did not use the same areas spatially at either a microhabitat or macrohabitat scale, and were only trapped at the same location once in 282 trap locations. Future conservation plans for the alligator snapping turtle and eastern snapping turtle should consider the microhabitat characteristics of sites used by these turtles.