Bacterial infections of the genitial tract are the major cause of reproductive failure in the mare. The variety of bacteria involved has been carefully established in the past and is approved in recent studies. There are approved laboratory procedures for etiologic diagnostics of bacterial infections of the female equine genital tract. Innovative molecular based approaches aim at elucidating, for instance, potential transmission modes of opportunistic pathogens like Pseudomonas aeruginosa, or at analysing genital microbial communities (microbiomes). The latter approach may provide new and more dynamic insights into the pathogenesis of genital infections since alteration of microbiomes is known to be associated with several pathogenic conditions.