Phylogenetic relationships among 20 species of extinct and living pikas (Ochotona) from Asia, Europe and North America were investigated by examining 38 cranial, mandibular and dental characters. Our data support phylogenetic distinction of three clades (Ochotona, Conothoa and Pika) recognized in recent molecular studies. Among the pikas of the subgenus Conothoa we found a lineage including three extinct species from Central Europe (in their number Ochotona kormosi sp. nov. from the Pleistocene of Hungary, described herein) along with extant O. roylei as a sister taxon. Our results suggest paraphyly of the subgenus Conothoa as currently understood. In addition, the steppe pika (O. pusilla) was recovered as a separate clade outside the monophyletic subgenera.

Our cladistic analysis is the first to examine phylogenetic placement of extinct forms within extant lineages of Ochotona. O. dodogolica is proposed as a member of Pika, O. polonica, O. kormosi and O. zabiensis as close to O. roylei, and O. nihewanica as a sister taxon to O. dauurica O. thibetana.

O. chowmincheni, a late Miocene species from China, proved a basal taxon, resembling Ochotonoides in the cranial and dental morphology, but lacking close affinities among Ochotona. According to our analysis, O. pusilla (with fossil O. gudrunae) belongs to the most basal clade of Ochotona, which supports the suggested antiquity of this lineage. Thus, we argue that of two morphotypes observed early in the evolutionary history of Ochotona, namely, the small species forms with minor p3 anteroconid versus large forms with enlarged p3 anteroconid with additional folds present, the former is more primitive and most probably evolved directly from the Bellatona—Bellatonoides lineage. Our results are in agreement with the known fossil record and we suggest the earliest Late Miocene of north China (Inner Mongolia and the adjacent regions) as the probable time and place of the origin of Ochotona.