Phylogeographic variation in mitochondrial (mt) DNA restriction sites is described for populations of the monotypic stinkpot turtle (Sternotherus odoratus) from the southeastern United States. Stinkpots display pronounced and hierarchical mtDNA phylogeographic differentiation, ranging from genetically shallow differences among local populations to genetically deep distinctions among regional assemblages of haplotypes. Both magnitude and general pattern of intraspecific mtDNA phylogeography in S. odoratus are remarkably similar to those in a related species (Sternotherus minor) that traditionally has been considered ditypic based on morphological and genetic appraisals. The pronounced phylogeographic population structure in S. odoratus effectively falsifies prior hypotheses that extensive dispersal and gene flow account for the morphometric conservatism among geographic populations. These findings also raise broader issues concerning the significance of subspecies designations in testudine systematics.