In the present study, the prevalence of mycotic endometritis (ME) in buffaloes and mares in district Faisalabad, Pakistan was investigated. Uterine flush samples were aseptically collected from 144 buffaloes and 75 mares and incubated on Sabouraud Dextrose Agar for two weeks. The overall prevalence of ME was 3.5% in buffaloes and 2.7% in mares. Ultrasonographically, buffaloes with ME had thicker endometrium (P<0.05) than that of buffaloes without ME (9.66±0.9460 mm vs 8.97 ± 0.0816 mm). Buffaloes bred through artificial insemination showed lower (P<0.05) incidence of ME than those bred through natural mating (2.3% vs 12.5%). In mares, stocking density (1.44% for 1-5 animals/paddock vs 33.3% for >10 animals/paddock), history of abortion and retained fetal membranes were significant risk factors (P<0.05) for the prevalence of ME. Management condition, body condition score and parity were not associated with the prevalence of ME in either species. In addition, herd size and reproductive problems had no effect on the prevalence of this problem in buffaloes. Antifungal susceptibility testing for buffalo isolates showed that all three isolated genera (Penicillium, Aspergillus and Rhizopus) were susceptible to itraconazole, Penicillium being the most susceptible. Penicillium and Aspergillus were resistant to fluconazole; however, Rhizopus was susceptible to fluconazole. In mares, out of the two isolates (Penicillium and Candida), Penicillium was susceptible to itraconazole and resistant to fluconazole, while Candida was resistant to both drugs. It is concluded that the prevalence of ME is not threatening in either species. However, buffaloes bred through natural mating; mares reared under high stocking density or those with history of abortion and retained fetal membranes have high risk of developing the disease.