Chlamydial infection in koalas causes conjunctivitis, rhinitis, urinary tract disease and female infertility. The chlamydial strains responsible have previously been designated as Chlamydia psittaci and have been subdivided into two types, I and II. In the present study we determined the DNA sequence of a 530 bp segment of the omp 2 gene from seven koala chlamydial strains, the type strain of C. pecorum, and the horse strain N16, and compared these with previously reported omp 2 gene sequences from 10 other chlamydial strains. Omp 2 sequence data clearly separated the seven koala strains into two genetic groups. Koala omp 2 group A corresponds to the previous type I designation and includes a conjunctival strain and a systemic disease-causing strain. The koala group A omp 2 sequence is 99% similar to the human C. pneumoniae IOL-207 strain and also 99% similar to the horse strain, N16. We propose that these koala strains be referred to as koala C. pneumoniae in future. Koala omp 2 group B corresponds to the previous koala type II designation and includes three urogenital tract strains plus two ocular strains. The koala group B omp 2 sequence is 99% similar to the C. pecorum type strain, VR628, while being only 77% similar to the EAE C. psittaci strain and only 71% similar to the koala group A strains. We propose that these koala strains be referred to as koala C. pecorum in future. The fact that two different species of Chlamydia infect koalas reinforces the observation that chlamydial species are not host restricted and makes us rethink the epidemiology of chlamydial disease in this marsupial.