Blood samples were taken from 541 small mammal captured in 2013–2015 in Znamensky district of Omsk region from Ixodes persulcatus and Ixodes trianguliceps sympatric area and examined for the Babesia spp. presence by nested PCR with subsequent sequencing of positive samples. Babesia microti DNA was found in 31,1 % of positive samples; a proportion of infected mammals varied from 5,3 % to 61,6 % in different sampling periods. B. microti DNA was found in samples from three prevailing Myodes species as well as from a root vole (Microtus oeconomus), field voles (Microtus argestis) and Siberian chipmunks (Tamias sibiricus). It was shown that identified B. microti samples belong to two genetic groups: B. microti ‘US’-type and B. microti ‘Munich’-type; notably that > 90 % infected mammals contained DNA of nonpathogenic for human B. microti ‘Munich’-type. We suppose that I. trianguliceps tick is the most probable vector of B. microti ‘Munich’-type.