The Vallarta Mud Turtle (Kinosternon vogti) was recently described based solely on morphological characters; therefore, an examination of molecular data to determine the validity of this species is warranted. Here, mtDNA barcodes, phylogenetic trees, and three Operational Taxonomic Unit (OTU) analyses offer new evidence to support K. vogti as a distinct lineage within the Kinosternon complex. We generated 1,237 base pairs of the mitochondrial cytochrome oxidase I and cytochrome b genes from two paratype specimens collected at the species' type locality in Puerto Vallarta, Jalisco, Mexico, and compared them with 20 other sequences from BLAST belonging to close relatives representing 16 species. From these sequence data, we estimated genetic p-distances, reconstructed phylogenetic relationships among taxa, and performed 3 different operational taxonomic unit analyses (CD-HIT-EST DNA, ABGD, and Bayesian Poisson Tree Processes). The mean genetic p-distances over all sequence pairs was 0.083 ± 0.00 substitutions per site, with the average number of base pair differences per site between K. vogti and all remaining sequences being 0.083 ± 0.009. The closest species to K. vogti were K. hirtipes (p-distances 0.057 ± 0.00) and K. scorpioides (p-distances 0.058 ± 0.00). Phylogenetic trees from maximum likelihood and Bayesian analyses of the concatenated data set showed the same topology with generally high node support. The 3 operational taxonomic unit analyses identified K. vogti as a distinct OTU and likely a distinct evolutionary lineage.