We examined the sequences of both rrn operons among the pathogenic non-cultivable treponemes, including 11 strains of T. pallidum ssp. pallidum, 5 strains of T. pallidum ssp. pertenue, 2 strains of T. pallidum ssp. endemicum, a simian Fribourg-Blanc and a rabbit T. paraluiscuniculi strain. We used PCR to determine the type of 16S-23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to 5 different genotypes. When compared to the T. pallidum ssp. pallidum strain, T. paraluiscuniculi Cuniculi A strain has a 17-bp deletion, and T. pallidum ssp. pertenue and endemicum and Fribourg-Blanc isolates show a deletion of 33-bp. Other than these deletions, we found only 17 heterogenous sites within the entire region (with excluding the 16S-23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded with the classification of treponemal strains, while two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be randomly distributed across the species/subspecies classification, time, and geographical source of the treponemal strains. We suggest that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.