Abstract: The microbial flora of fishes raised in different earthen ponds at African Regional Aquaculture centre, Aluu, Rivers State, Nigeria, were examined. The skin, gills and gastro-intestinal tract of Clarias gariepinus, Oreochromis niloticus, Hybrid (cross of Heterobranchus bidorsalis and Clarias gariepinus) were examined. Fourteen species of bacteria, 8 types of fungi and 6 types of parasites were identified. Escherichia coli, Aeromonas hydrophila, Acinetobacter sp., Pseudomonas fluorescens were the most frequently isolated microorganisms. Gram-positive microorganisms: Bacillus sp. Corynebacterium sp. Staphylococcus sp., were also consistently isolated. Micrococcus luteus and Clostridium perfringes occurred variably. Gyrodactylus sp., Dactylogyrus and Trichodina were consistently isolated. The public health and economic significance of the findings were discussed.