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Aim Pikas ( Ochotona spp.) are alpine specialists that show considerable morphological and genetic variation structured along latitudinal and elevational gradients. Recent studies of North American and Asian pikas have uncovered phylogeographical partitioning among separate mountain ranges and drainages, driven by Quaternary climate fluctuations. We tested the prediction that collared pikas ( O. collaris) exhibit lower genetic diversity and less structure than other species of pika due to lower long-term habitat stability. Location Eastern Beringia ( Alaska and north-western Canada). Methods We examined phylogeographical variation in the collared pika ( O. collaris) throughout much of its known range using the mitochondrial cytochrome b gene. Population divergence and genetic diversity were compared within and between mountain ranges. Genetic diversity was contrasted with current and Pleistocene habitat fragmentation inferred from ecological niche models. Results Low but significant differentiation was evident between most populations of O. collaris, with little haplotype sharing among populations and a single phylogeographical break separating a genetically distinct haplogroup in the south-eastern part of its range. Variation was mostly structured within populations (as opposed to between populations or mountain ranges). When within-species nucleotide diversity in O. collaris, O. princeps and O. curzoniae was compared, genetic diversity was found to decline with increasing latitude. Main conclusions Populations of O. collaris are less geographically structured and exhibit less variability than populations of either O. princeps or O. curzoniae. This pattern is better explained by the amount of available Pleistocene habitat predicted for each species than by current predicted habitat or population discontinuity. Collared pikas are currently considered to be a common species at low risk of extinction, but their habitat specificity, population subdivision, and low genetic variation may have consequences for their continued viability in a warming world. [ABSTRACT FROM AUTHOR]