An investigation was conducted to determine the presence of fungi in C. gariepinus harvested from selected farms and dams in Zaria and its environs. A total of 360 randomly sampled Clarias gariepinus (African mudfish) and 144 fish holding water samples were collected from three dams (wild captured) and three fish farms (cultured). They were screened for fungi using Sabouraud Dextrose Agar as isolation medium. Identification of the fungi was done by macroscopic observation of the growth morphology followed by microscopy after staining with lactophenol cotton blue. Four fungal genera namely; Mucor (12.50%), Aspergillus (18.06%), Tricophyton (5.56%) and Penicillium spp. (4.17%) were isolated from water samples. Similar fungi were also isolated from the fish skin swabs in the following order; Mucor spp. (49.57%), Aspergillus sp.(31.30%), Trichophyton sp.(10.43%) and Penicillium sp.(8.0%). Finding these fungi in the fish holding water might have occurred through the use of contaminated and/or decomposed feed, from runoffs, waste water discharges from nearby human settlements into the aquatic environment. The infection of fish by the isolated fungi diminishes both the aesthetic and economic value of fish. Attention must therefore be paid to fish hygiene and fish health management practices must be upheld. We hereby recommend that fish meant for human consumption be properly exposed to temperature high enough to eliminate contaminating fungi.