The Chlamydiales are a family of unique intracellular pathogens that cause significant disease in humans, birds and a wide range of animal hosts. Of the currently recognized species, Chlamydophila (previously Chlamydia) pneumoniae, unlike the other chlamydial species, has been previously considered to be solely a pathogen of humans, causing significant respiratory disease and has also been strongly connected with cardiovascular disease. Here we report the finding that strains of C. pneumoniae are widespread in the environment, being detected by molecular methods in a range of reptiles (snakes, iguanas, chameleons) and amphibians (frogs, turtles). Of particular interest was the finding that genotyping of the chlamydial major outer membrane protein gene in these newly identified C. pneumoniae strains showed that many were genetically very similar, if not identical to the human respiratory strains. Whether these reptilian and amphibian strains of C. pneumoniae are still capable of infecting humans, or crossed the host barrier some time ago, remains to be determined but may provide further insights into the relationship of this common respiratory infection with its human host.