Background: The prolonged retention of progesterone-infused intravaginal sponges in estrous synchronization protocols, results in alteration of vaginal microflora, disturbance of vaginal pH, and increased vaginitis in goats. These changes lead to the growth of opportunistic pathogenic bacteria, such as Escherichia coli and Staphylococcus aureus, which need antibiotics to treat this condition. Probiotics have recently been suggested as an alternative method for the maintenance of vaginal health and improving animal fertility. Aim: To investigate the effects of probiotics (Lactobacillus plantarum and L. acidophilus), in compared with enrofloxacin and a control group, on vaginal microflora, vaginal pH, vaginitis incidence, and fertility in Black Iraqi goats synchronized with the progesterone intravaginal sponges. Methods: Thirty adult black Iraqi goats, aged (2-4) years, were randomly divided into three separate groups, each group (n= 10). The first group received progesterone sponge only (control). The second group received progesterone sponges combined with 50 mg of intravaginal enrofloxacin. The third group received progesterone sponges combined with probiotic suspension (2×109 CFU/sponge L. plantarum and L. acidophilus). Vaginal swabs were collected prior to sponge insertion (Day 0) and immediately after sponge removal (Day 14), for bacterial isolation, pH measurement and cytological evaluation of vaginitis. Pregnancy diagnosed by ultrasound 28±3 after mating. Statistical analysis was performed using ANOVA and chi-square tests. Results: The incidence of vaginitis was significantly increased (P<0.05) in all groups, observed 80%, 60%, and 50% in the control, enrofloxacin, and probiotic groups, respectively. The mean vaginal pH increased significantly in all groups (P<0.001) was highest in the control group (8.1±0.16) and lowest in the probiotic group (6.9±0.12) (F2, 27=9.73; P<0.05) after sponge removal. Escherichia coli was most predominant in all groups; it increased 90% in the control group and declined to 30% (P<0.05) and 40% (P<0.05) in the enrofloxacin and probiotic groups, respectively. Lactobacillus spp. increased to 70% in the probiotic group though not significantly (P>0.05). The pregnancy rates were 50% in the control group and 80% in both treated groups, with a highly significant difference among groups (χ²= 57.6; P<0.01). Conclusion: The application of the intravaginal probiotic modified vaginal microflora, maintained vaginal pH, decreased vaginitis and improved animal fertility. The probiotic efficacy was comparable to enrofloxacin without destroying beneficial bacteria.