We established the phylogeny of 11 species of the genus Marmota based on the entire sequence of the mitochondrial cytochrome b (cyt-b) gene (1.1 kb) and a partial sequence of the NADH dehydrogenase subunit 4 (ND4) gene (1.2 kb). In three species (Marmota caligata, Marmota olympus, and Marmota bobac) full-sized nuclear pseudogenes of the mitochondrial cyt-b were identified. The mitochondrial cyt-b genes and the three pseudogenes form separate clusters in the maximum parsimony dendrogram. This finding suggests that the pseudogenes originated from a single transfer to the nucleus that may have occurred prior to the radiation of the genus Marmota. Notably, compared with their functional mitochondrial equivalents the pseudogenes show a much lower substitution rate. In the dendrograms deduced from the mitochondrial sequences two distinct clusters become apparent: one cluster consists of the North-west American species, the other contains the Eurasian species together with the North American species Marmota monax. The position of M. monax as a member of the Eurasian clade is in accordance with the evolution of chromosome numbers. The results are of special interest with respect to the evolution of social systems in the genus that vary from solitary species (M. monax) to highly social species living in family groups (e.g. Marmota marmota). The molecular phylogeny suggests a diphyletic origin of high sociality in the genus Marmota.