Despite being one of the world's 25+ most endangered tortoises and freshwater turtles, the evolutionary history of the Vietnamese pond turtle (Mauremys annamensis) is largely unknown. This is due to the lack of wild, known-locality specimens for genetic studies. In this genetic study, we include four known-locality specimens of M. annamensis—two historical specimens (the lectotype and paralectotype of the junior synonym Annamemys merkleni), a living zoo specimen that was collected in 1966, and a contemporary, wild-caught specimen captured during intensive field surveys. We have three major findings regarding the genetics of M. annamensis and closely related species. First, with wild specimens from near the type locality, we identify mitochondrial and nuclear haplotypes for true M. annamensis. Second, we verify that M. guangxiensis is invalid due to its non-monophyly. Lastly, we verify that M. mutica from Anhui Province and Taiwan cluster genetically with samples from the type locality in Zhejiang Province. Despite these new data from known-locality specimens providing guidance for ex situ and in situ conservation efforts, some of the genetic patterns for M. annamensis and M. mutica defy obvious explanation and highlight the need for even more samples with reliable known provenance.