Although it was originally described as a species, it was reevaluated by Musser in 1969, who determined it to be a subspecies of the Zempoaltepec deer mouse (Habromys lepturus). Another evaluation by Carleton et al. in 2002 of H. lepturus and the other species of the genus Habromys determined significant morphological differences between H. lepturus and H. ixtlani, and H. ixtlani was reclassified as a separate species.
Musser, G. G. and M. D. Carleton. 2005. Superfamily Muroidea. pp. 894–1531 in Mammal Species of the World a Taxonomic and Geographic Reference. D. E. Wilson and D. M. Reeder eds. Johns Hopkins University Press, Baltimore.