There is some taxonomic debate surrounding this species, with some authors considering Baeodon a genus rather than a subgenus.

Thomas noted that the eponym for the species name "alleni" was Harrison Allen, calling him "the chief authority on North-American bats.

"[2] In 1906, Gerrit Smith Miller Jr. placed Allen's yellow bat into a newly-coined genus, Baeodon.

[3] At present, some authors keep Allen's yellow bat as part of Rhogeessa within the subgenus Baeodon,[4] while others believe that it is distinct enough that Baeodon should be considered a monotypic genus rather than a subgenus.

[1] However, most records of this species are at elevations greater than 1,000 m (3,300 ft) above sea level.