Rock-dwelling pikas of the genus Ochotona have fragmented montane geographical distribution presumably associated with geological and climatic events of Late Quaternary. Within this genus, the northern pika, O. hyperborea has the widest distribution. Taxonomic composition and subspecific structure of this species has been controversial during the past century. Sixteen available names were combined in different manners into a variable number of weakly overlapping subspecies by previous authors. A comparison of data sets from the entire distribution range of northern pikas is presented here for the first time, including: craniometric, bioacoustic, and multilocus genetic data. We examined 301 skulls, and the mitochondrial COI gene and two nuclear introns in 79 specimens, as well as the structure of alarm calls from 107 individuals. Our results show that the six subspecies within O. hyperborea correspond to the six genetic parapatric lineages. Five of these are hypothesized to be involved in hybridization at the edges of their distribution. Three acoustic races completely correspond with the six genetic lineages: each acoustic race consists of two lineages. Morphometric data do not display any phylogenetic signal in our study. The subspecies from the Mountains of Khabarovsk Territory, north of Amur River, is described de novo as O. h. fedoseevi ssp. n. The type locality of O. hyperborea is defined more accurately. A neotype is designated for O. h. cinereofusca to stabilize use of names of pikas from the Amur region.