Subgenus Alexandromys (Pavlinov et al., 1995a; Pavlinov and Rossolimo, 1998). Also variously included in subgenus Pallasiinus (Zagorodnyuk, 1990) or subgenus Microtus (Gromov and Erbajeva, 1995; Gromov and Polyakov, 1977; Meyer et al., 1996). Meyer (1983) considered M. middendorffii to be phylogenetically distant from other northern and central Asian species of Microtus, but close relationship to M. oeconomus broadly supported by analyses of allozymes (Mezhzherin et al., 1993), karyology and morphology (Meyer et al., 1996), and DNA sequences (Conroy and Cook, 2000a). Vorontsov and Lyapunova (1976) considered M. middendorffii (and hyperboreus) to be chromosomally closely related to North American M. miurus, but cytochrome b sequences group M. middendorffi with M. fortis and Palaearctic species, not M. miurus and North American endemics (Conroy and Cook, 2000a). Karyotype documented by Boyeskorov et al. (1993, as hyperboreus).

The taxon hyperboreus has been widely treated as a separate species (Gromov and Erbajeva, 1995; Gromov and Polyakov, 1977; Meyer, 1983; Musser and Carleton, 1993; Pavlinov and Rossolimo, 1987; Pavlinov et al., 1995a). Corbet (1978c) included hyperboreus in M. middendorffi based on Gileva’s (1972) demonstration of their complete interfertility. Meyer et al. (1996) comprehensively marshalled chromosomal, morphological, and hybridization data that sustain inclusion of hyperboreus as a subspecies in M. middendorffii, along with typical middendorffii and ryphaeus.