Chlamydia psittaci is a broad host range pathogen with avian hosts acting as major reservoirs. Zoonoses are acquired via inhalation and are usually linked to contact with birds or contaminated substrates. C. psittaci infections in mammalian species other than humans have been less well-studied with prevalence rates potentially underestimated. In Australia, cases of equine reproductive loss have recently come under the spotlight due to apparent zoonotic transmission of C. psittaci from equine placental membranes to humans, a previously unrecognised route of transmission for this organism. We investigated the role and genetic identity of C. psittaci strains involved in an epizootic of equine reproductive loss and associated zoonoses in New South Wales using molecular and genomic approaches. A total of 199 cases of equine reproductive loss from 55 properties across NSW were examined. Placental and foetal swabs were tested for C. psittaci using real-time PCR to determine infection prevalence. To determine whether C. psittaci was likely to be responsible for equine reproductive loss, tissue samples were examined by in situ hybridisation, and chlamydial loads were also determined by qPCR. Finally, genome sequencing was undertaken from clinical samples to determine the strain of C. psittaci associated with equine abortion and associated zoonoses. The prevalence of C. psittaci infection detected in this study across all cases on all properties was 21.6%. C. psittaci was detected at 21 out of 55 properties sampled and found to be clustered around Scone and Wagga Wagga. Significantly more properties in the Scone area had C. psittaci positive cases compared to those outside that area, suggesting an abortion cluster. Genome sequencing and MLST typing of isolates from Scone and Wagga Wagga suggested that equine C. psittaci isolates were clonal and belonged to the globally distributed 6BC cluster known to be associated with Australian psittacines. In situ hybridisation confirmed the presence C. psittaci within equine tissues and the median load of C. psittaci was significantly higher in placental membranes compared to foetal tissues (P < 0.01). High chlamydial loads (> 1 × 106 organisms/mg of tissue) were detected in samples collected during this study, including those from the zoonosis-linked index case. These results suggest that equine chlamydiosis may have resulted from spillover of infection from native parrots, that C. psittaci likely plays a role in equine reproductive loss and that infected foetal membranes frequently carry a sufficient load of C. psittaci to pose a potential risk to human health.