This paper describes the characterization and taxonomic status of N16, a chlamydial isolate from the respiratory tract of a horse. N16 contains plasmid DNA, has normal elementary body morphology and its inclusions do not stain with iodine. Its major outer-membrane protein (MOMP) gene was completely sequenced and compared with the MOMP genes of Chlamydia pneumoniae, C. psittaci, C. trachomatis and C. pecorum. This analysis revealed that N16 is closely related to the TWAR strain of C. pneumoniae (94.5% and 94.4% DNA homology with TWAR isolates IOL-207 and AR-39 respectively). By comparison, N16 shows between 72.1% and 73.7% DNA homology with C. psittaci strains, 70.9% and 71.1% homology with C. pecorum strains LW613 and 1710S and 69.2% homology with C. trachomatis serotype E. The MOMP gene of N16 shares 93.8% DNA homology with the MOMP gene of a chlamydial isolate KC from the conjunctiva of a koala. Monoclonal antibodies raised to C. pneumoniae IOL-207 and shown to be C. pneumoniae-specific confirmed that N16 was more closely related to C. pneumoniae than to C. psittaci. Thus DNA homology and monoclonal antibody data both suggest that horse chlamydiae, as exemplified by N16, form a new second strain of C. pneumoniae. This species is probably more widespread and diverse than the current literature would suggest.