The Mesoamerican slider Trachemysvenusta is endemic to Central America and Southern Mexico. Several human-mediated disturbances, including habitat degradation and illegal hunting for food, have impacted its populations along the Usumacinta river basin. The extent to which these disturbances have affected the genetic diversity and population structure of T. venusta inhabiting the basin remains unresolved. To this end, we analyzed eight microsatellite markers in five wild populations of T. venusta from the middle and lower reaches of the basin as well as one captive population. Our results show high levels of genetic diversity for all analyzed populations, low F ST values, high gene flow and no genetic structure, indicating an absence of genetic differentiation across sites and, thus, a single panmictic population for the basin. Evidence of a genetic bottleneck was observed in two of the wild populations (and the captive one), indicating some impact from disturbances, whether from poaching or habitat fragmentation, despite the seemingly high connectivity of most populations. Results are discussed in terms of the relative importance of genetic parameters for the conservation of T. venusta, particularly in light of the importance of demographic stochasticity in local conditions undergoing rapid changes.