Although originally proposed as separate species, many authors previously considered both the black-chested and Beaudouin's snake eagles to be subspecies of the short-toed snake eagle (Circaetus gallicus). However, this convention was not followed by all taxonomists, with some citing differences in adult plumage and breeding ranges as evidence in favour of awarding each full species status. Brown (1974) followed this latter view, but cited several instances of alleged hybridization between the three forms which would justify their treatment as a single species under the Biological Species Concept. However, Clark (1999) suggested that these alleged hybridization events may have instead resulted from misidentification of juvenile or subadult black-chested snake eagles as adults of other species.
A molecular phylogenetic analysis based on two mitochondrial genes and one nuclear intron showed that the Circaetus snake eagles form a monophyletic group that is sister to the Old World vulture group, Aegypiinae. This study also suggested that the black-chested snake eagle was more closely related to the brown snake eagle (Circaetus cinereus) than to the short-toed snake eagle, supporting its taxonomic recognition as a separate species. However, a different molecular phylogenetic study by Wink and Sauer-Gürth (2004) found that the black-chested and short-toed snake eagles form a clade together with the bateleur (Terathopius ecaudatus). The black-chested snake eagle is thus commonly considered to form a superspecies with the short-toed and Beaudouin's snake eagles.