The aim of this study was to identify the vaginal bacteria flora in black Iraqi goats subjected to estrus synchronization. Sixteen multiparous black Iraqi goats presented in the farm of the College Veterinary Medicine, Al-Anbar University, were included in this study, during the breeding season, from May 2011 to July 2011. The ages of the animals rwere 2-4 years. A polyurethane sponge containing 20 mg of micromsed cronolone (fluorogestone acetate progestagen) was inserted in the vagina for 14 days. Standard bacteriological procedures were performed on vaginal mucus swabs obtained before application of the sponges and at sponges withdrawal. Results of this study revealed that the most bacterial flora was Gram positive Bacilli before insertion of sponges, while most of Gram negative Bacilli were present after sponges withdrawal. Bacterial culture of vaginal swabs taken before insertion of sponges showed 8 isolates (50%) G _ and 8 isolates (50%) G + , while after withdrawal of sponges the bacterial culture showed 10 isolates G _ (45.4%) and 12 isolates (54.6) G + . The most prevalent bacteria isolated were S. aureus (10 isolates) 26.3%. E. coli (6 isolates) 15.8%, P. vulgaris (6 isolates) 15.8%, C. (4 isolates)10.5% and other bacteria where having 2 isolates 5.2% for each one includes, Entercoccus fecalis, Entrococcus, Entrobacter, Klebsiella pneumonia, Pseudomonas aeroginosa and Salmonella. In conclusion, using progestagen impregnated sponges in the vagina for estrus synchronization could stimulate inflammation of the vaginal mucous membrane and increase of bacterial infection.