We investigated the usefulness of rRNA gene restriction fragment length polymorphism (RFLP) for grouping of the Borrelia isolates associated with Lyme disease or from ixodid ticks. Genomic DNA was digested with a restriction enzyme, blotted and hybridized with an rrl (23S rRNA) gene probe. The sizes of the restriction bands showed a good correlation with the genotypes recently proposed, and Borrelia isolates of diverse geographic origin formed four distinct DNA groups. Group I included all of the USA isolates and some European isolates; group II contained European isolates and Asian isolates; group III comprised European and Asian isolates; group IV included Japanese isolates and an eastern Russian isolate. Groups I, II and III corresponded to Borrelia burgdorferi, B. garinii and group VS461, respectively. The RFLPs of Japanese isolates were rather divergent and some of the isolates were quite distinct from the USA and European isolates. RFLP analysis of the rRNA genes and flanking regions, using rrl gene probes as we reported here, may be useful in the taxonomic study of Borrelia.