Phylogenetic relationships within a group of Paleartic short tailed ground squirrels (Spermophilus), recently defined as genus, are not sufficiently clear and need a critical revision. Interspecies hybridization, found in Eurasian Spermophilus, can affect the results of reconstruction of molecular phylogeny. Alashan ground squirrel position on the phylogenetic tree needs clarification. We analyzed eight nucleotide sequences of cytb gene of S. alashanicus and 127 sequences of other Spermophilus species form GenBank. S.alashanicus and S. dauricus close phylogenetic relationship, and their affinity to ancestral forms of the group are revealed. Monophyly of Colobotis subgenus was confirmed. Paraphyly of eastern and western forms of S. relictus was shown.