Geographic variation was studied in the south-east Asian turtles of the genus Malayemys (Testudines: Bataguridae). Discriminant function analysis of head-stripe and shell characters reveals a clear pattern of geographic variation that is consistent with the topography of south-east Asia and the poor dispersal abilities of these turtles. Two phenotypically and morphologically distinct groups of Malayemys occur allopatrically in lowland areas of mainland south-east Asia, and my data concludes that each should be recognized as a distinct species. Turtles from the Mekong River Basin retain the name Malayemys subtrijuga (Schlegel and Müller, 1844), whereas those from the Chao Phraya and Mae Klong river basins, coastal areas of south-eastern Thailand, and the Malay Peninsula are assigned the name Malayemys macrocephala (Gray, 1859). Malayemys macrocephala has four or fewer nasal stripes (99%) and an infraorbital stripe that is relatively wide at the loreal seam (98% of InfSW/HW=0.07-0.18) and does not extend or extends only slightly superior to the loreal seam (96%). Conversely, M. subtrijuga has six or more nasal stripes (89%) and an infraorbital stripe that is relatively narrow at the loreal seam (92% of InfSW/HW=0.02-0.06), extends completely superior to the loreal seam (96%), and usually joins the supraorbital stripe (64%). Female M. macrocephala also have relatively longer AnL and relatively shorter Vert5L and PecL than M. subtrijuga. Similarly, male M. macrocephala have relatively longer PPLL and AbdL, relatively shorter Pleu1L and PecL, and greater RLatK values than M. subtrijuga. Both species are potentially threatened by overcollection and habitat destruction, and should be protected as separate taxa of concern. In addition, discriminant function analysis of shell and head-stripe characters suggests that M. subtrijuga on Java are derived by human intervention primarily from the Mekong River Basin.