Summary Endometritis is recognised as one of the major causes of reproductive failure, specifically infertility and abortions, in mares. Infectious agents are the most common cause of endometritis, mainly bacteria. Here, we describe a case of an unexplained reproductive failure caused by an uncommon bacterium, A. hippocoleae, in a 15‐year‐old Thoroughbred mare with an oscillating reproductive history from Southern Brazil. Strain A. hippocoleae_LBV077/21 was isolated from the mare's uterus swab and identified by MALDI‐TOF (Matrix‐Assisted Laser Desorption Ionisation – Time of Flight) and 16 S rDNA sequencing. The antimicrobial susceptibility test showed that the strain was susceptible to ampicillin, ceftiofur, cephalexin, ciprofloxacin, rifampicin, penicillin, sulfamethoxazole/trimethoprim, tetracycline and vancomycin. Partial 16 S rDNA sequence phylogenetic analysis indicated a well‐supported position of A. hippocoleae_LBV077/21 in an exclusive clade of A. hippocoleae, whilst all other Arcanobacterium species were positioned in a separated clade, highlighting the lower syntenic relationship of the species A. hippocoleae to the other Arcanobacterium species. The present study reaffirms the importance of the isolation and identification of infectious agents in mares in cases of reproductive failure because uncommon agents can impede successful treatment and the improvement of reproductive failures.