We evaluated the taxonomic status of snakes from the Atractus emmeli species complex (composed by A. boettgeri, A. emmeli, A. paravertebralis, and A. taeniatus) on the basis of concordance between quantitative (meristics and morphometrics) and qualitative (pholidosis, color pattern, and hemipenis) analyses of morphological characters, in combination with ecological niche modeling and niche overlapping. We synonymize A. boettgeri, A. paravertebralis, and A. taeniatus with A. emmeli based on the congruent analytical results. We also describe a new species to accommodate the Brazilian populations from the state of Mato Grosso mainly based upon some unique states of morphological characters, including hemipenial morphology, color pattern, and meristics. We found that the new species has a distinct ecological niche compared with A. emmeli and some level of niche overlapping with A. albuquerquei. We found great differences in ecological niches of species occurring in the Cerrado versus those occurring in the Western Amazon–Andean foothills, suggesting a putative niche evolution in this group.