The distribution and genetic diversity of 91 of Beauveria isolates collected during a long-term survey in boreal forests of northern European Russia was studied. Based on morphological and sequence analysis of TEF and Bloc loci, three Beauveria spp. were identified: B. pseudobassiana, B. bassiana, and B. caledonica, with abundance of 81, 11, and 8%, respectively. Through multilocus sequencing, four haplotypes of B. bassiana and two haplotypes of B. caledonica were detected. Twelve haplotypes of B. pseudobassiana with non-random distribution were identified. Two haplotypes of B. pseudobassiana were the most abundant and widespread occurring across the whole study area, whereas others tended to be more specific to either the north or south of the study area, indicating the presence of different subpopulations. For further analysis of these putative subpopulations, southern and northern areas were separated along the boundary of the Köppen–Geiger climate zones (dfb and dfc), and the genetic structure was examined by analysis of molecular variance and spatial autocorrelation. Molecular evidence of intraspecific recombination of B. pseudobassiana and B. bassiana across northern European Russia area was indicated.