Albert Günther originally described the species in 1867 after Frederick DuCane Godman and Osbert Salvin collected specimens in Central America. In 2007, the species was moved from the genus Archocentrus to a new genus, Amatitlania based on Juan Schmitter-Soto's study of Archocentus species. However, a 2008 study led by Oldrich Rican proposed moving the species in Cryptoheros and Amatitlania, including Amatitlania nigrofasciata into the genus Hypsophrys.
A number of synonyms exist for this species including: Archocentrus nigrofasciatus, Cichlasoma nigrofasciatum, Cryptoheros nigrofasciatus and Heros nigrofasciatus