Species of genus Chlamydia are important pathogens of animals, with a worldwide distribution and broad host range. Some species, such as Chlamydia psittaci, also pose a zoonotic disease risk. Abortion is one of the many diseases that has been associated with chlamydial infections in animals, with most attention focused on the economic impacts to sheep production. The role of chlamydia in equine abortions is unknown. Using the family-specific 23S ribosomal RNA (rRNA) Chlamydiaceae real-time PCR, we tested 169 formalin-fixed, paraffin-embedded fetal membrane samples from 162 equine abortion cases collected between 2000 and 2018 in Switzerland. Two equine abortion cases (1.2%) tested positive for Chlamydiaceae. Further analyses by the species-specific 23S rRNA ArrayMate microarray and sequencing of a fragment of the 16S rRNA gene revealed C. abortus and C. psittaci. In both cases, equine herpesvirus 1 was also present, which might have been the abortion cause, alone or in synergy with Chlamydia. The prevalence of abortigenic chlamydial species in equine abortion cases in our study was significantly lower than rates described elsewhere. Zoonotic chlamydial agents present in equine fetal membranes nevertheless should be considered a potential risk to humans during foaling, abortion, or stillbirth.