A new species of Atractus, previously reported as a disjunct population of A. zidoki south of the Amazon River, differs from all congeners in having an undivided sulcus spermaticus. Herein, we restrict the concept of A. zidoki to populations north of the Amazon River, provide a detailed description of its everted hemipenis, and describe a new species to accommodate the population occurring to the south of the Amazon River. Additionally, we briefly discuss intraspecific variation and the systematic value of the hemipenis structure in snakes, mainly with respect to the genus Atractus.