A possible explanation for endometritis in mares is ascendant contamination from the vagina. The presence of Lactobacillus spp. is considered to be important in women for a healthy vaginal environment; however, there are few studies in mares related to the presence of Lactobacillus in the vaginal flora of healthy mares. The present work aims to determine the occurrence of Lactobacillus spp. in the vaginal micro-environment of mares. A total of 35 crossbred multiparous mares, aged between 4 and 12 years, with no history of reproductive problems and with healthy reproductive tracts, were used. Two vaginal swabs were obtained from the mares during estrus for Lactobacillus isolation and PCR evaluation. Ten human female volunteers, aged between 24 and 35 years, sexually active, with no history of gynecological diseases and treatments in the past two years were used. Lactobacillus spp. were isolated from 5.7% of the mares’ vaginal samples and from 90% of the women’s vaginal samples. Lactobacillus DNA was detected by PCR in 22.9% of the mares’ vaginal samples and in all of the vaginal samples from the healthy women. The primers used here were demonstrated to have in silico specificity for the detection of L. equi (AB425924.1), L. pantheris (DQ471798.1) and L. mucosae (DQ471799.1), but they did not anneal on Enterococcus faecalis (EU887827.1) or E. faecium (EU887814.1). In conclusion, this study showed a low occurrence of Lactobacillus spp. in mares, suggesting that this bacterium may not play a fundamental role in the equilibrium of the vaginal micro-environment of normal mares.