We determined nearly complete flagellin gene sequences for Borrelia burgdogeri sensu lato isolates (11 isolates obtained from Ixodes persulcatus ticks and patients in Hokkaido, Japan, and 1 European isolate) representing six different restriction fragment length polymorphism (RFLP) ribotype groups following cloning of the PCR-amplified genes. These sequences were aligned with those of representatives of the three Borrelia species associated with Lyme disease, and a phylogenetic tree was constructed by the Clustal method. On the Lyme disease borrelia portion of the tree, the species were clearly delineated into three different phylogenetic groups, in complete agreement with the division of B. burgdogeri sensu lato into three species. A phylogenetic analysis revealed that the representatives of FWLP ribotype groups IV, V, and VI clustered tightly with each other and belonged on the same branch as Borrelia garinii. We used the criteria that are currently used to delineate bacterial species and determined the levels of DNA relatedness for these Borrelia isolates. For the RFLP ribotype group IV, V, and VI isolates, the levels of DNA relatedness ranged from 79 to 88%, and the levels of relatedness to the reference strain of B. garinii ranged from 70 to 80%. The levels of DNA relatedness of the RFLP ribotype group IV, V, and VI isolates to the representatives of other species associated with Lyme disease ranged from 53 to 66%. All of these findings indicate that the RFLP ribotype group IV, V, and VI isolates should be included in the species B. garinii.The following three validly described Borrelia species are associated with Lyme disease: Borrelia burgdogen sensu stricto, Borrelia garinii, and Borrelia afielii (5,8,21). Although the distribution of B. burgdogeri sensu stricto is rather restricted in North America and Europe, B. garinii and B. afielii are widely distributed in all of the north temperate regions of the world except North America. It has been generally assumed that Ixodes ricinus species complex ticks are major vectors for transmitting infections to humans and that the spirochetes are maintained by vector-reservoir transmission cycles involving blood-sucking ticks and wildlife vertebrates (1,2,6,20).A large number of spirochete strains have been isolated from patients exhibiting erythema migrans, Ixodes persulcatus ticks, and reservoir rodents (Apodemus speciosus) in the northern part of Japan, where Lyme disease is endemic (4,12,14,22,26, 28, 30). Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis, Western blot (immunoblot) analysis with monoclonal antibodies, the restriction fragment length polymorphism (RFLP) ribotyping method, and a 16s rRNA gene-based PCR assay, we have demonstrated that these isolates exhibit considerable phenotypic and genetic heterogeneity (12,14, 32, 33). No B. burgdoifen sensu stricto isolate has been found in the material examined so far in Japan. Some of the isolates were classified as B. garinii or B. afzelii strains by our typing methods, while the oth...