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The heterogeneity of the Ixodes persulcatus population in the vicinity of Saint Petersburg was estimated by using malate dehydrogenase (MDH) isoenzyme. There are six MDH genotypes carrying 3 alleles in the Ixodes persulcatus population. The prevalence of Borrelia and Ehrlichia species in the study genotypes was analyzed. There was a difference in the prevalence and intensity of infection. The greatest abundance of Borrelia was described in the genotypes to Genogroup 1 (with allele 1). Among them, heterozygous ticks were most intensively infected. Polymerase chain reaction identified species pathogenic for man. These included 3 species of Borrelia: B. afzelii, B. garinii, and B. burgdorferi sensu stricto and 2 species of Ehrlichia muris and HGE agent. The author are the first to describe HGE agent and B. burgdorfei ss encountered in Russia.