The species Daptrius ater was first described by Louis Jean Pierre Vieillot in 1816. It previously shared its genus with the red-throated caracara, which is now known as Ibycter americanus in the monotypic genus Ibycter. The inclusion of I. americanus in the genus Daptrius was made by ornithologist Herbert Friedmann in 1950, and backed up by Dean Amadon in 1968. However, a recent mitochondrial DNA and nuclear sequence data study focusing on caracaras and allies (subfamily Polyborinae) determined that these two species not only differ in genus, but are also arranged in polyphyly, meaning that they do not share a common most recent ancestor. Additionally, it was concluded that D. ater's closest relative is the yellow-headed caracara (Milvago chimachima), existing on the phylogenetic tree as a sister group.
