This study was conducted at the College of Education for Pure Sciences (Ibn Al-Haitham), University of Baghdad. The aim of this study was to isolate and diagnose fungi from fish feedstuff samples, and also detection of aflatoxin B1 and ochratoxin A in fish muscles and feedstuffs. Randomly, the samples were collected from some fish farms from Baghdad, Babil, Wasit, Anbar, and Salah al-Din provinces. This study included the collection of 35 feedstuff samples and 70 fish muscle samples, and each of the two fish samples fed on one sample of the feedstuff. The results showed the presence of several genera of different fungi including Aspergillus spp, Mucor spp., Penicillium spp., Yeast spp., Fusarium spp., Rhizopus spp., Scopiolariopsis spp., Epicoccum spp., Alternaria spp., Cladosporium spp., Botrytis spp., Helminthosporium spp. and Trichtheicum spp. Aspergillus spp. was the most present in all feedstuff samples by 48%, while the results of the detection of aflatoxin B1 showed contamination in 53 samples of the total 70 samples of fish muscles, while the contamination was found in 34 samples of fish feedstuff from a total of 35 samples. The concentrations ranged from 0-310 ppb in muscles and ranged from 0-864 ppb feedstuffs. Results of the detection of ochratoxin a revealed that 17 of the fish muscle samples were contaminated with the toxin of the total 70 samples and contamination of 13 feedstuff samples of the total 35 feedstuff samples. The concentration of ochratoxin A ranged from 0-98 ppb in fish muscles, while in feedstuffs it ranged from 0-573 ppb.