The southwestern woolly rat belongs to the subgenus <Anteliomys> of the genus <Anteliomys>, and its species-level status is stable. There are currently 4 subspecies under the species, all distributed in Yunnan. The nominate subspecies <E. c. custos> (Thomas, 1912), the type locality is Deqin, Yunnan; the Lijiang subspecies <E. c. rubelius> (Allen, 1924), the type locality is Yulong Snow Mountain, Lijiang, Yunnan; the Cangshan subspecies <E. c. cangshanensis> Wang et Li, 2000, the type locality is Cangshan, Dali, Yunnan; the Ninglang subspecies <E. c. ninglangensis, Wang et> Li, 2000, the type locality is Ninglang, Yunnan.
