Brackish water fishes usually harbour human pathogenic bacteria particularly the enterics and coliform groups in their mucosal surfaces. Thus, this study was undertaken to investigate the prevalence of skin and gills microbiota of Tilapia guineensis as to understand their microbial assemblages and as well provide useful insights into the broad dynamics of the fish host-microbial relationship and health status. Thirty samples of Tilapia guineensis were collected from Buguma brackish water environment, River State, Nigeria. The skin and the gills of the tilapia were analyzed microbiologically. Specimen were collected by swabbing aseptically over the skin and gills segment of the fish and then processed for total bacterial count, followed by isolation and identification of isolated bacteria. Microbial load analysis revealed that the total viable count of bacteria ranged from 2.4 to 7.6 x 105 cfu/ml for skin and 2.1 to 5.7 x 106 cfu/ml for gills, and it was observed to fall within the recommended microbiological standard safety limit. A total of thirty-seven (37) bacteria, belonging to fifteen different genera in the family of Vibrionaceae, enterobacteriaceae and Morganellaceae were isolated from the fish. The prevalent rate of the bacterial shows that Proteus vulgaris recorded the highest frequency of occurrence of 16.22%, followed by Vibrio parahaemolyticus with 10.81% occurrence and Provindencia rettgeri, Serratia mercescens and Salmonella sp. trailed them with 8.11%. Kluyyera ascorbate, Citrobacter amalonaticus, Proteus mirabilis, Enterobacter aerogenes, plesiomonas shigelloides and Pseudomonas sp. have the least frequency of occurrence with 2.7% respectively for each. Though the bacterial count of Tilapia guineensis harvested from the water and fish sample did not exceed the standard recommended safety limit. There were several potential pathogenic and spoilage bacteria isolated as part of the fish flora. The presence of these bacteria could poses or constitute a public health risk.