The current study aimed to isolate and diagnose the fungi associated with the inflammatory bowel disease patients with 150 samples distributed between 50 samples from Crohn's patients and 50 samples from ulcerative colitis patients, 50 control from Al-Kindy Al Teaching Hospital in Baghdad, Baghdad. Five types of yeast were isolated and identified, namely C. albicans, C.glabarta, Tropicales, C. parapsilosis, C. and C., krusi C. parapsilosis and.and Aspergillus, Penicillium, Muocer, Rhizopous, Saccharomycosis, and Cryptococcus, The results indicated the dominance of Candida spp. In crohn’s disease, the frequency of isolated Candida albicans was 24 (58.54%), Candida glabrata 11 (26.86%), Candida tropicalis 5 (12.2%) and Candida krusi was 1 (2.44%); the statistical analysis detected a significant differences (<0.001) in the frequency of isolated Candida in this disease and the higher ratio was with Candida albicans On the other hand, the frequency of candida species in Ulcerative colitis patients was as following: Candida albicans 15 (45.45%), Candida glabrata 6 (18.18%), Candida tropicalis 11 (33.3%) and Candida parapsilosis i 1 (3.03%) The results found that there is a significant differences between the ratio of the isolated Candida species and the high frequency was with Candida albicans. They were confirmed by PCR device, The C. albicans showed the ability to form a Grem tube and Chlamydospore formation. Cultivation on the differential medium, chromo agar, showed that the yeast of C. albicans in a light green color, C.tropicalis in a metallic blue, and C.parapsilosis in a creamy white color as the C .krusei was light pink in color, while C.glabrata was pinkish-purple in color. Isolation and diagnosis of these species have been confirmed by the Vitek2 Compact System. Four types of antifungal agents fungi Nystatin Clotrimazole Fluconazole Itraconazole. The results of the PCR using the fungi starter pair (ITS1, ITS4) showed that they produced different molecular sizes ranging from (510-870) bp