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Objective:To isolate and identify microflora and fungal species at different phases during estrus synchronization of ewes and estimate their prevalence; compare the effectiveness of antimicrobial administration to intravaginal sponge on the changes in the vaginal micro-organisms and reproductive performance.Methods: Sixty Egyptian ewes were allocated into three equal groups (G: 1, 2 and 3). G1 was inserted with vaginal sponge containing medroxy-progesterone acetate and served as control; without antimicrobial additive. The other two groups were treated as G1, but sponges were previously injected with ciprofloxacin (G2), while sponges of G3 were injected with ciprofloxacin and clotrimazole. Vaginal swabs were collected from each treated ewe, prior sponge insertion, at sponge withdrawal and 48 h later for microbiological investigation and bacterial count. On the day of sponge removal, 300 IU/eCG was administered for each treated ewe. The identified bacterial strains before sponge insertion were tested for sensitivity with antimicrobial disks.Results:Bacterial isolates before sponge insertion were more sensitive to ciprofloxacin. Frequencies of ewes in estrus; the interval from sponge withdrawal to onset estrus and the duration of estrus were statistically similar among treated groups. The pregnancy rate in G2 (100%) was higher than G1 (66.7%) and G3 (82.4%). The total bacterial count before sponge insertion was similar between all treatments and increased significantly in all groups on the day of sponge withdraw. The prevailing bacteria on D0, D14 and 48 h after sponge removal for all treated groups wereStaphylococcus spp. followed byEscherichia coli. Regarding to fungus species, percentages of isolation increased from 5% (before sponge insertion) to 100.00% and 88.89% at sponge withdraw for G1 and G2, respectively. In G3, the fungus was declined from 10% (before sponge insertion) to 5% (at sponge removal).Conclusions:The concomitant treatments by antimicrobial to the vaginal sponge which used for estrus synchronization in ewes can improve reproductive performance.