Subgenus Alexandromys (including Pallasiinus, as per Zagorodnyuk, 1990, and Pavlinov et al., 1995a) or subgenus Microtus (Gromov and Polyakov, 1977). Phylogenetic interpretation of cytochrome b sequences allies M. montebelli in a tight clade with M. fortis, M. middendorffii, M. kikuchii, and M. oeconomus (Conroy and Cook, 2000a); karyotypic information also indicates special relationship to M. oeconomus (Borodin et al., 1997; Zagorodnyuk, 1990). Other chromosomal data summarized by Tsuchiya (1981) and Satoh and Obara (1995). Gastric musculature documented by Ohuchi et al. (1992). Corbet (1978c) included Sikotan Isl in the Kuriles within the species range, but this record is erroneous (Kawamura, 1988, and references therein).

Kawamura (1988, 1991, 1994) exhaustively summarized molar variation of Holocene and middle-late Pleistocene samples and defined Quaternary species endemic to Japan. Microtus montebelli, now the only surviving Japanese endemic, then occurred with populations of M. epiratticepoides and M. cf. brandtioides (perhaps = M. fortis; see Kaneko and Hasegawa, 1995), both of which disappeared between 15,000 and 10,000 years before present.