One reason that the genus is complex is because of the species' variable karyotypes:[2] *Note that R. tumida is listed four times, as individuals have been found with four different karyotypes.

[12] However, others argue that as Allen's yellow bat and the slender yellow bat are sister taxa, to exclude only one from Rhogeessa makes it a paraphyletic group.

By that logic, either both species need to be included in Rhogeessa, or both need to be placed in Baeodon.

[2] A 2008 paper recommended moving the slender yellow bat to the Baeodon genus.

[2] Others say that Baeodon should be recognized as a subgenus of Rhogeessa instead of as a separate genus.