This study intends to explore the prevalence of pathogenic bacteria infected the vaginal cavity of sheep and goats, in addition to determine the normal vaginal bacterial flora in pregnant and non pregnant local breed goat and sheep. Vaginal swabs were collected from 80 cases comprised of 54 sheep and 26 goats that involve 20 and 6 pregnant ewes and goats from Baghdad city during May 2019 to July 2019. These samples were cultivated onto different bacteriological media. The isolated bacteria were identified by different biochemical tests. Mixed bacterial isolates were determined in 65 out of 80 (81.3%) samples. Totally, 9 various microorganisms were isolated from animal’s vagina. E. coli, Streptococcus Spp, KlebsiellaSpp and Staphylococcus aureus were the most common isolated microorganism from vaginal swabs in a percentage of 36, 20, 17.5 and 16.3%respectively. While Bacillus Spp, Proteus Spp, Staphylococcus Spp, Corynebacterium Spp and Salmonella Spp.were the less common isolated microorganisms in a percentages of 10, 10, 7.5, 6.3 and %2.5 respectively. Moreover, the enteric bacteria especially E. coli was isolated in the higher incidence rate (44.4%) in pregnant ewes compared to pregnant goats 15.4%. However, in non-pregnant animals, the percentages were 50 and 15% in sheep and goats respectively. Nonetheless, Proteus Spp were isolated only from newly birth animals. Meanwhile, Staphylococcus aureus were relatively isolated at the same level of incidence at 15%-17% in either pregnant or non-pregnant sheep or goats, while Streptococcus Spp were mostly found in pregnant goats and ewes at 50 and 25% respectively. In conclusion, this study approved the isolation of different bacterial spp in various incidence rates from vaginal cavity of pregnant and non-pregnant sheep and goats.