Subgenus Alexandromys (Zagorodnyuk, 1990) or subgenus Microtus (Gromov and Polyakov, 1977; Meyer et al., 1996; Pavlinov and Rossolimo, 1987). Most researchers view this species as phylogenetically close to M. mongolicus (Meyer, 1983; Meyer et al., 1996; Radjabli et al., 1984). Zagorodnyuk (1990) listed M. fortis as the only member of its species group and related to the M. middendorfii group, which contains M. middendorffii, M. miurus, M. mongolicus, and M. sachaliensis. This association is supported by allozymic analysis (Mezhzherin et al., 1993); data integrated from chromosomal, morphological and hybridization studies (Meyer et al., 1996); and phylogenetic analysis of cytochrome b, also including M. montebelli, M. kikuchii, and M. oeconomus (Conroy and Cook, 2000a). Chromosomal variation and its significance assessed by Kovalskaya et al. (1988, 1991).

Kaneko and Hasegawa (1995) reported M. fortis and M. oeconomus from late Pleistocene cave deposits on Miyako Isl in the Ryukyu Isls, and claimed that the late Pleistocene samples from continental China, other Ryukyu Isls, and Honshu, Japan identified in the literature as brandtioides, epiratticeps, and complicidens (not necessarily the holotypes, which were not studied) actually represent M. fortis (modern range does not include Japan or the Ryukyu Isls). According to Zheng and Li (1990), specimens identified as brandtioides, epiratticeps, and complicidens from China are a mixed assemblage. At Choukoutien, e.g., the oldest fossil (early Pleistocene) is true brandtioides, fragments from other sites are nearly indistinguishable from living Lasiopodomys brandti, specimens called epiratticeps may represent more than a single species, complicidens is in a different genus (Hexianomys), and M. fortis is present but had been misidentified as brandtioides. Zheng and Li (1990) regarded true brandtioides to be a species of Lasiopodomys, as did Repenning (1992).