Sometimes viewed as a Nearctic member of Chionomys (Anderson, 1959), or allocated to subgenus Microtus (Chaline, 1974; Hall, 1981), or to subgenus Aulacomys (Zagorodnyuk, 1990). Although strongly differentiated relative to other North American Microtus (e.g., Hooper and Hart, 1962; Modi, 1987; Moore and Janecek, 1990), the phyletic affinity of M. longicaudus lies with this complex and not Old World Chionomys (Chaline and Graf, 1988; Conroy and Cook, 2000a; Gromov and Polyakov, 1977; Zagorodnyuk, 1990).

Extensive karyotypic (Judd and Cross, 1980) and molecular (Conroy and Cook, 2000b) variation reported, albeit not necessarily concordant, which invites continued taxonomic investigation. Well-defined geographic groupings of cytochrome b haplotypes interpreted in light of Pleistocene climatic changes, possible refugia, and likely isolation during northward reexpansion along different colonizing routes (Conroy and Cook, 2000b). Finley and Bogan (1995) discussed the inconsistent usage and problematic identification of subspecies (alticola, mordax, and longicaudus) in NW Colorado, an area which tellingly circumscribes some of the most distinctive populations (Southern Rockies Clade) identified by Conroy and Cook (2000b) and whose genetic divergence approaches that of other Microtus species. Includes coronarius, which Jones et al. (1986) viewed as an insular derivative and subspecies of M. longicaudus; MacDonald and Cook (1996) continued to list coronarius as species and advised broader comparisons with M. longicaudus populations to vindicate its status. See Smolen and Keller (1987, Mammalian Species, 271).