This genus is systematically complex and sometimes controversial. 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. This may represent a species complex.[10][2]
Some have placed Allen's yellow bat into its own genus, Baeodon based on its differences with other members of the genus.[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.[9][13]