The distribution of the highly diversified and species-rich snake genus Atractus was assessed in search for endemism areas. The dataset of 6000 museum specimens was used to run an Endemicity Analyses in order to identify areas of biogeographic relevance for the genus Atractus. By using distinct methodological approaches and modifying the size and shape of grid cells we obtained a better adjustment to each species range, taking into account species distributed along the Andean and Atlantic Forest mountain ranges or certain vegetation constraints. Three scales of endemism were observed: micro endemic areas, represented by three different regions; intermediate sized endemic areas, represented by nine different regions; and macro-endemic areas, represented by four different provinces. Although most assessed regions corroborate well-defined biogeographic units according to the scientific literature, some, mainly located in the Colombian Andes, are not regularly considered in biogeographic syntheses carried out for vertebrates. Methodological approaches, along with a well curated database and taxonomic accuracy, may significantly influence the recovery of endemism areas, mainly considering mountain topography and local niche structure. The results present herein highlight the relevance of three Colombian Cordilleras, in order to completely understand Neotropical biota patterns of distribution. It is important to note that a well-resolved taxonomy represents both the framework and the first step toward a comprehensive biographical synthesis reducing Wallacean shortfalls in biodiversity.