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We surveyed the natural distribution of Borrelia species associated with
Lyme disease in the subalpine forests of Nagano prefecture, Japan, during 1993-94. Tick-derived isolates (n = 112) from Ixodes persulcatus and rodent-derived isolates (n = 55) from Apodemus argenteus, Apodemus speciosus, Eothenomys andersoni, Eothenomys smithii, and Microtus montebelli were classified by rRNA gene restriction fragment length polymorphism analysis (RFLP ribotyping). Ribotype group IV (an intraspecific variant of Borrelia garinii) was predominant among the tick isolates. It was also isolated repeatedly from the rodents. Ribotype group III (Borrelia afzelii) was detected in low frequencies among the tick and rodent isolates. The data suggest that humans are likely to be exposed to the group IV when they are bitten by I. persulcatus ticks.