We studied for the first time the molecular differentiation of all three currently recognized subspecies of Trachemys scripta, including the morphologically distinct western populations of T. s. elegans ('western red-eared sliders'), using mitochondrial and nuclear DNA sequences (up to 3,236 bp and 2,738 bp, respectively) and 14 microsatellite loci. We found that only the quickly evolving microsatellite loci discriminated T. s. troostii and the western red-eared slider from the remaining two subspecies, while T. s. elegans and T. s. scripta were not distinct in any marker system. Our findings challenge the current intraspecific systematics of T. scripta and suggest that the conspicuous differences in coloration and pattern reflect population-specific, rather than taxonomic, differentiation. We abstain from synonymizing any subspecies because, for traditionalists and conservationists, abandoning the well-established and morphologically distinct subspecies of T. scripta is not desirable. However, if subspecies of T. scripta continue to be recognized, the current taxonomy with three subspecies is difficult to justify. Western red-eared sliders are morphologically distinct and differ from T. s. elegans and T. s. scripta, with respect to microsatellites, as much as T. s. troostii does. In view of this morphological and genetic evidence, subspecies status should be considered for western red-eared sliders.