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Borrelia spirochetes were isolated from the adult ixodid tick (Ixodes persulcatus) in three areas of far eastern Russia, namely, Khabarovsk, Vladivostok, and Yuzhno-Sakhalinsk. Borrelia infective rates of ticks in those areas were 24.5, 41.4, and 25.1%, respectively (total rate was 26.6%). Spirochetes were also isolated from the tissues of small mammals captured at Khabarovsk (infective rate was 20.8%). Samples were classified by rRNA gene restriction fragment length polymorphism (RFLP) analysis. The isolated spirochetes from ticks were classified mainly RFLP ribotype group IV (B. garinii), followed by groups II (B. garinii), III (B. afzelii), and V (B. garinii), showing that B. garinii is a dominant species among them. Both B. garinii and B. afzelii were also found in rodents, and multiple infections with those two species were observed in some rodents. B. burgdorferi sensu stricto (group I) was not isolated from either ticks or rodents.