Originally named as a species of Evotomys, later included in the synonymy of C. rufocanus smithii (Ellerman and Morrison-Scott, 1951), and eventually revised by Aimi (1980) as a species of Eothenomys. Subsequently arranged as a species of Phaulomys (Musser and Carleton, 1993), Eothenomys (Kaneko, 1994), or Clethrionomys (Pavlinov et al., 1995a). Evidence for treatment under Myodes is explained in account of M. smithii. Species reviewed by Kaneko (1994, as Eothenomys).
Kaneko et al. (1992a) documented vertical distributions, zone of overlap (650-1325 m), and morphological separation of M. andersoni (alpine habitats generally above 1000 m) and M. smithii in C Honshu (also see Kimura et al., 1994, 1999). Honshu specimens of problematic identification can be confidently associated using Y-chromosome morphology, certain external proportions and cranial traits, and mammae formula (Iwasa, 2000; Iwasa and Tsuchiya, 2000). G-band chromosomal homologies between M. andersoni and M. rufocanus documented by Obara (1986). Junior synonymy of niigatae, occasionally treated as specifically distinct, clarified by Aimi (1980) based on morphological traits. His conclusion is strongly corroborated by cross-breeding experiments (Kitahara and Kimura, 1995), analyses of mitochondrial and nuclear ribosomal DNA (Suzuki et al., 1999b), and C-banding comparisons of the Y chromosome (Iwasa and Tsuchiya, 2000); however, Kaneko (1994) continued to recognize niigatae as a valid species occurring in C Honshu.