Samples were transported from Maiduguri to the microbiology Laboratory, Department of food Science Technology of the University of Agriculture, Makurdi in sterile polythene bags for microbial analysis. Portions of the skin surface, gills and tissue of all the samples were cut and 1g of each sample was weighed out and homogenized in sterile test tube containing 9ml of distilled water which became the stock solution (1:10 dilution). Serial dilutions were then made up to 10^-9 and 10ml. The result of this study showed that pathogenic bacteria and fungi are present in smoked C. gariepinus sold in Maiduguri markets. The study also revealed that a total of eight (8) types of microbes [three (3) species of bacteria and five (5) species of fungi] were isolated from the samples of smoked C. gariepinus. The bacteria observed include, Eschericia coli, Staphylococcus aureus and Salmonella spp. The fungi present in the fish samples were Fusarium spp., Mucor spp., Aspergillus fumigatus, Aspergillus niger and yeast. Majority of the fungal isolates identified in this study produces mycotoxins. The presence of fungi particularly aflatoxigenic molds in these fish species is very significant as it was indicated by food safety standard that aflatoxigenic molds produce mycotoxins which have pathogenic effects on man. The result of this study shows that, Baga road market had highest microbial contamination (1.567 x 10^{3 ±} 0.243 x 10³ cfu/g), and Gamboru market recorded the lowest, 0.806 x 10^{3 ±} 0.131 x 10³ cfu/g. However, there was no significant difference in terms of microbial load between Gamboru market and Abbaganaram market (0.806 x 10^{3 ±} 0.131 x 10³ cfu/g and 0.841 x 10^{3 ±} 0.105 x 10³cfu/g respectively). Reverse was the case in Gamboru and Abbaganaram markets whose environments were at least the most hygienic of all the markets under study and this translates to their relatively low microbial load. In conclusion, microbial contamination or re-contamination of smoked catfish products has been seen to vary from one locality (market) to another and even within the same locality from one fish processor or seller to another. To enhance consumers’ health, the use of mechanized smoking system that would completely dehydrate the fish in order to prevent contamination due to moisture is recommended. Also authorities such as National Agency for Food and Drugs Administration and Control (NAFDAC) should look into the environmental condition of our food handlers as it concerns the smoking factories, the markets and even the hawkers that carry the food from one place to another.