The species Rhabdosoma microrhynchum (now Atractus microrhynchus) was originally described based on a single specimen collected by the Orton Expedition at "Guayaquil," in the Guayas province on the Pacific coast of Ecuador. The holotype is currently lost and all specimens previously referred to this species were misidentified on the basis of material from Peruvian Amazonia. While examining museum collections and conducting fieldwork in the Pacific lowlands of Ecuador and Peru, we found specimens assignable to A. microrhynchus. In this study, we report the morphological variation in these new specimens of A. microrhynchus and evaluate the taxonomic status of the Amazonian species previously confused with it. We restrict the concept of A. microrhynchus to the Pacific lowland populations from Ecuador and Peru, and we designate a neotype for the species. Based on the examination of the types of A. emersoni and A. natans from Amazonia, we found that there is wide overlap in the internal and external characters of both taxa. Therefore, A. emersoni is relegated to the synonymy of A. natans. Furthermore, we compared A. microrhynchus with all congeners and discuss its affinities with the A. multicinctus species group based on shared, exclusive hemipenial features. © 2012 by The Herpetologists League, Inc.