Two species of Dasyprocta are currently recognized in Colombia. However, the taxonomic history of this genus is complex, with several available names for different populations. Here, we explore intra and interspecific variation of the two species currently recorded in Colombia, D. fuliginosa y D. punctata, and evaluate whether morphological characters allow the separation between specimens from different geographical regions. In addition, we clarify the application of subspecific names to different populations in the country and the distribution patterns of D. punctata subspecies. We show that D. fuliginosa and D. punctata are allopatric in Colombia. D. fuliginosa is distributed in the Amazon, Orinoco and part of the North Andean regions (eastern foothills of the Eastern Cordillera), whereas D. punctata is found in the Caribbean, Chocó and western foothills of North Andean regions of the country. Although there are no clear morphometric or morphological differences in the skull between most taxa, different coat colorations are associated with different geographical regions and contrasting ecosystems. D. punctata candelensis is distributed in the High Magdalena River Basin, North-Andean Province, instead of the Chocó Region as suggested by other authors. D. punctata chocoensis is found in the Colombian Pacific coast and western foothills of the Western Cordillera; D. punctata colombiana is found in the northern part of Colombia in the Caribbean Region. We also found specimens matching the description of D. punctata zuliae from the North-Andean Province in the Eastern Cordillera of Colombia. Despite the present geographic differences in coloration, further revisionary work—including genetic approaches—is needed to further understand the diversity of the genus in Colombia.