Colombia has a high diversity of continental chelonians, being a hot spot for this group of vertebrates. However, most species are in some threat category and do not present enough information to assess their real threat status. In this study, potential distribution spaces were estimated for seven genetic lineages of the Rhinoclemmys melanosterna continental tortoise species, with the purpose of generating information to contribute to conservation actions of the same and its habitat. For this, a maximum entropy algorithm and geographic and climatic information are used. The study revealed that several genetic groups of the species have differential abiotic conditions and therefore different areas of distribution. The areas of distribution revealed correspond to some Colombian freshwater ecoregions, suggesting population isolation and limited genetic flow between the genetic groups in each eco region. Additionally, the study suggested the presence of an unidentified genetic clade in the Jurado River. The generated models will be a starting point to propose conservation areas for the different genetic groups, thus preserving their genetic diversity and evolutionary potential in melanosterna Rhinoclemmys.