Objective: The unhygienic nature of our local markets, including fish handlers, may contribute to the presence of microorganisms in smoked fish leading to food poisoning. Furthermore, heavy metals can find their way into the food chain through fish raising public health concerns. This study assessed the microbial load and some heavy metals in smoked fishes (bongafish and catfish) sold in urban and rural markets in Akwa Ibom State, Nigeria. Materials and Methods: Standard microbiological techniques and analytical procedures were used for microbial and heavy metals analyses, respectively. Results: The results revealed that all the smoked fish obtained from the two markets were contaminated with heavy metals and microorganisms. Zinc was the most frequently detected heavy metal in both fish types (catfish: 15.50 ± 9.99 mg/kg; and bongafish: 16.40 ± 12.28 mg/kg) obtained from urban market, while in the rural market, it was cadmium (catfish: 15.95 ± 10.15 mg/kg; and bongafish: 18.25 ± 7.15 mg/kg). The overall elemental concentrations of the heavy metals in the fishes were in decreasing order of Cadmium>Zinc>Nickel>Cobalt>Lead. The most predominant bacterial species in fishes from the urban market was Bacillus subtilis (7.5 × 104 ± 0.871 colony- forming unit/g) while Candida tropicalis (9.2 × 104 ± 0.105) was the most predominant fungal species. More bacteria and fungi were encountered in fishes from the rural market than from the urban market. The differences in the microbial loads from the two markets were not statistically significant (P > 0.05). Conclusion: There is a potential health risk of eating smoked fishes that are poorly stored or handled in the market as a result of heavy metal contamination and the presence of the pathogenic organism. Therefore, maintenance and enforcement of adequate sanitation practices in these markets should be encouraged to avert unpleasant health consequences.