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A phylogeographical study of the northern three-toed jerboa, Dipus sagitta, which has one of the largest geographical ranges among Palaearctic desert rodents, was performed using complete mitochondrial cytochrome b (Cytb) and fragments of two nuclear genes. Phylogenetic analysis of the Cytb data, including 222 specimens from 69 localities revealed, six allopatric lineages divergent at 7.4-10.1%. In some lineages the Cytb data are supported by nuclear data, thus confirming a high level of cryptic diversity within D. sagitta. The recovered pattern of genetic differentiation was reviewed from a taxonomic perspective. In general, the mitochondrial lineages show relatively good correlation with morphological subspecies. Both mitochondrial and nuclear data support the isolated position of the Qaidam lineage, which diverged from the rest in the Early Pleistocene (similar to 1.5 Myr) according to our molecular clock results. Therefore, we propose to recognize this lineage as a separate species, Dipus deasyi; the taxonomic status of other lineages remains to be clarified. The results are consistent with the hypothesis that the centre of the origin of the D. sagitta complex is located in the eastern part of the range. The geographical structure of genetic variation in D. sagitta is compared to those in other desert rodents.