Map turtles of the genus Graptemys are highly aquatic and rarely undergo terrestrial movements, and limited dispersal among drainages has been hypothesized to drive drainage-specific endemism and high species richness of this group in the southeastern United States. Until recently, two members of the megacephalic “pulchra clade,” Graptemys barbouri and Graptemys ernsti, were presumed to be allopatric with a gap in both species' ranges in the Choctawhatchee River drainage. In this paper, we analyzed variation in morphology (head and shell patterns) and genetics (mitochondrial DNA and microsatellite loci) from G. barbouri, G. ernsti, and Graptemys sp. collected from the Choctawhatchee River drainage, and we document the syntopic occurrence of those species and back-crossed individuals of mixed ancestry in the Choctawhatchee River drainage. Our results provide a first counter-example to the pattern of drainage-specific endemism in megacephalic Graptemys. Geologic events associated with Pliocene and Pleistocene sea level fluctuations and the existence of paleo-river systems appear to have allowed the invasion of the Choctawhatchee system by these species, and the subsequent introgression likely predates any potential human-mediated introduction.