Cryptic or undescribed species pose a major problem in conservation biology. Managing multiple unresolved taxa collectively as a single entity could precipitate the loss of unrecognized genetic variation and unique populations and, possibly, lead to extinction of undiscovered or unrecognized taxa. In contrast to other species in its clade, the Pascagoula map turtle (Graptemys gibbonsi), as currently recognized, is not confined to a single major river system (or a cluster formed by a major river and adjacent minor drainages) but occurs in two major river systems, the Pearl and Pascagoula Rivers. We analyzed G. gibbonsi samples from both rivers for the first time in a morphological and molecular assessment of the taxonomic status of this poorly studied species. We compared the extent of genetic differentiation (mitochondrial DNA; mtDNA) between G. gibbonsi populations with members within the pulchra clade and between Graptemys oculifera and Graptemys flavimaculata. We found significant carapace pattern variation and morphological differentiation between the Pearl and Pascagoula river samples of G. gibbonsi. Our mtDNA sequences showed greater genetic differentiation between G. gibbonsi samples from the Pearl and Pascagoula rivers than between two recognized and reciprocally sympatric species, G. oculifera (Pearl River) and G. flavimaculata (Pascagoula River), but revealed only a modest degree of differentiation when compared to other members of the pulchra clade. Based on the degree of differentiation in 1) morphology, 2) color patterns, and 3) mtDNA, in addition to their 4) allopatric distributions, we describe a new species from the Pearl River, restricting the species G. gibbonsi to the Pascagoula River.