The aim of this work was to identify the fungal isolates present in the genitalia of the repeat breeding mare and application of acriflavine and normal saline as an intrauterine lavage for its treatment. A total number of 75 mixed bred mares were introduced to the Vet. Teaching Clinic, Assiut University, Department of Theriogenology between January 2007 and December 2008 included in this study. These animals had clinically normal genitalia but failed to conceive after at least 3 times of natural mating. Out of them, 40 mares showed positive mycotic infection. The mares were treated twice with one week interval. According to treatments the animals divided into four groups, 10 mares for each. First group (G1) was treated with saline, second group (G2) treated with acriflavine dissolved in distilled water in concentration 1:1000, third group (G3) treated with streptomycin 2 gm and the fourth group (G4) left without treatment. After the second treatment, all mares were left for one cycle then mated with highly fertile stallion then pregnancy diagnosis was done using ultrasonography at 30-45 days after mating. The obtained results revealed that, the common isolates genera from the swabs were Aspergillus (37.33%), Acremonium (20.82%), Paecilomyces (11.11%), Fusarium (9.33%), Penicillium (7.55%), Mucor (5.33%), Alternaria and Drechslera (2.22% each),), Trichothecium and Cladospotium (1.78% each), and Candida (0.004%). The most common Aspergillus subspecies were A. fumigatus and A. niger. The detectable mycotoxins were Alfatoxine B1, B2, G as well as Aflatoxine B1 and B2, Citrinin and Zearalenone which were extracted from A. flavous, A. terrus, A. parasiticus and Fusarium oxysporum, respectively. The conception rates were 40%, 60%, 10%, 0% in G1, G2, G3 and G4 group, respectively. Therefore, it could be advised that the use of sterile physiological saline and/or diluted acriflavine could be indicated to counteract such sort of genital fungal infections successfully.