Phylogenetic relationships among 43 bacterial strains of Xanthomonas and two strains of Stenotrophomonas maltophilia were clarified by PCR-restriction fragment length polymorphism (RFLP) analyses of three DNA fragments corresponding to 16S, 23S rDNA and the 16S-23S rRNA internal transcribed spacer region (ITS) using ten restriction enzymes. From the data of the 16S rDNA RFLPs, seven genotypes were detected, while eight genotypes were observed based on the data of the 23S rDNA RFLPs among Xanthomonas strains tested. When the data of the 16S and 23S rDNA RFLPs were combined, the Xanthomonas strains were divided into thirteen rDNA genotypes. Cluster analysis based on rDNA genotypes showed that they were divided into two groups designated as subgroups 1 and 2, which were distinguishable from the related genus Stenotrophomonas. On the basis of the ITS RFLPs, 20 types were observed, and two groups were formed. The members of each group were the same as those based on the rDNAs. The data suggests that this genus is phylogenetically grouped into at least two lineages.