The phylum was first designated as Cushitic around 1858. Historical linguistic analysis and archaeogenetics indicate that the languages spoken in the ancient Kerma culture of what is now southern Egypt and northern Sudan, as well as those spoken in the Savanna Pastoral Neolithic culture of the Great Lakes region, likely belonged to the Cushitic branch of the Afroasiatic family.
The positions of the Dullay languages and of Yaaku are uncertain. They have traditionally been assigned to an East Cushitic branch along with Highland (Sidamic) and Lowland East Cushitic. However, Hayward thinks that East Cushitic may not be a valid node and that its constituents should be considered separately when attempting to work out the internal relationships of Cushitic.
Cushitic was formerly seen as also including the Omotic languages, then called West Cushitic. However, this view has been abandoned. Omotic is generally agreed to be an independent branch of Afroasiatic, primarily due to the work of Harold C. Fleming (1974) and Lionel Bender (1975); some linguists like Paul Newman (1980) challenge Omotic's classification within the Afroasiatic family itself.
Additionally, historiolinguistics indicate that the makers of the Savanna Pastoral Neolithic (Stone Bowl Culture) in the Great Lakes area likely spoke South Cushitic languages. Christopher Ehret (1998) proposes that among these languages were the now extinct Tale and Bisha languages, which were identified on the basis of loanwords. Ancient DNA analysis of a Savanna Pastoral Neolithic fossil excavated at the Luxmanda site in Tanzania likewise found that the specimen carried a large proportion of ancestry related to the Pre-Pottery Neolithic culture of the Levant, similar to that borne by modern Afroasiatic-speaking populations inhabiting the Horn of Africa. This suggests that the Savanna Pastoral Neolithic culture bearers may have been Cushitic speakers, who were gradually absorbed by neighboring hunter-gatherer communities in the lacustrine region.