Cambodia is known to harbour three distinct species of Southeast Asian leaf turtles (Cyclemys spp.), which are heavily traded and common in seizures of wildlife. Confiscated leaf turtles are often released to natural habitats. Thus, an exact knowledge of the distribution of the individual species is of great importance to avoid the introduction of non‐native turtles, posing the risk of competition and hybridization. In this study, we examine a recently discovered leaf turtle population from Phnom Kulen National Park using external morphology, 17 unlinked microsatellite loci and the mitochondrial cytochrome b gene. Leaf turtles from the Phnom Kulen National Park morphologically resemble C. oldhamii, but harbour mitochondrial haplotypes of C. atripons. With respect to microsatellite loci, the turtles are distinct from C. atripons. Unfortunately no material of C. oldhamii was available from Cambodia. We propose that the Phnom Kulen population represents either a natural hybrid swarm of C. atripons and C. oldhamii or a distinct undescribed species with introgressed mitochondria of C. atripons. This underlines that genetic differentiation of wild leaf turtle populations in Cambodia is complex and suggests that this differentiation pattern becomes increasingly threatened by translocations of confiscated individuals. For drawing a definite conclusion about the taxonomic status of the Phnom Kulen population, denser sampling of other Cambodian leaf turtle populations would be required, in particular of C. oldhamii.