As a way of checkmating public health implication associated with processed fish products, the study was conducted to assess the bacterial load and diversity in the fillets of smoked Atlantic mackerel, Scomber scombrus sold in major fish markets (Anua, Useh, Etuk, Itam and Akpan-Andem) in Uyo, Akwa Ibom State. Determination of bacterial loads, species characterization and composition in fish fillets were done using standard microbiological procedures. Results from the study revealed the highest fungal counts of 9.0x104cfu/ml in samples from Itam market. Heterotrophic bacteria count ranged from 2.0x106 cfu/ml in Useh market samples to 2.5x106cfu/ml in samples from other study sites. A total of eleven bacterial and six fungal species were recovered. Salmonella enterica and Shigella sonnei accounted for the highest frequency of occurrence (100%) in all the study sites while Escherichia coli and Vibro cholera had 80% prevalence. Serratia liquenfaciens, Bacillus subtilis, Lactobacillus plantarum, Micrococcus luteus and Bacillus cereus recorded 40% occurrence while the least prevalence of 20% was recorded in Staphylococcus albus and Proteus mirabilis. The isolated fungal species were Penicillum expansum (60% prevalence), Aspergillus flavus, Mucor hiemalis, Rhizopus stolonifer and Geotriculun candidum (40%) while A. fumigates (20%). Bacterial flora recovered in this study composed of potential pathogenic organisms of public health interest. This calls for intensified monitoring efforts towards controlling fish food contamination in Uyo metropolis.