Until 1997, atrinucha was grouped into the larger "Slaty Antshrike" Thamnophilus punctatus sensu lato complex, a suite of more than 11 taxa distributed from Belize to south to southeastern Brazil. Following an analysis of geographic variation in plumage and vocalizations by Isler et al. (1997), the punctatus complex was broken into no fewer than six separate species. Of these, the Western Slaty-Antshrike T. atrinucha is the northernmost member of the complex, and is the only member of the group that is distributed west of the Andes.
Thayer and Bangs (1905) described the population from Gorgona Island, off the west coast of South America, as a separate subspecies, gorgonae. This subspecies is similar to nominate atrinucha, but in the male the forecrown is more extensively gray, and the underparts are lighter gray. Female gorgonae by a darker color on the underparts (with the throat only slightly paler than the breast), a more rufous back, and a much darker crown (Cory and Hellmayr 1924, Zimmer and Isler 2003). Recordings of the vocalizations of gorgonae are not known, and so this taxon was not included in the analysis of geographic variation by Isler et al. (1997).