Investigation into the microbiological quality, proximate and mineral content of three smoked fish species obtained from three markets in Benin City. The fish samples were identified as Oreochromis aureus (Blue tilapia), Scomber scombrus (Atlantic mackerel) and Gymnarchus niloticus (Trunk fish). Total heterotrophic bacteria and fungi count, coliform count and staphylococcal counts were carried out using standard microbiological procedures. The isolates were identified using both phenotypic and molecular methods. Comparative nutritional estimation of the proximate of moisture, crude protein, fibre, ether extract, dry matter, ash content and gross energy were determined using standard analytical chemical methods. Mineral composition of Fe, Mg, Zn and Ca were determined using atomic absorption spectrophotometer (AAS) while Na and K were by flame photometry. The total heterotrophic bacterial count was in the range of 6.20 ± 0.27 x10⁵ to 7.33 ± 0.58 x10⁵ (cfu/g) while the coliform count was in the range of 3.26 ± 0.43 x10⁴ to 4.26 ± 0.43 x10⁴ (cfu/g). The Staphylococcal count was in the range of 2.07 ± 0.43 x10⁴ to 2.76 ± 0.43 x10⁴ (cfu/g). The bacteria isolated were Escherichia coli strain NBRC 102203-54, Serratia marcescens strain TRL, Staphylococcus aureus strain RFI22, Bacillus cereus strain PM-2, Morganella morganii subsp. sibonii strain ML and Enterobacter cloacae PD2. Fungi isolated were Aspergillus niger, Fusarium oxysporum, Saccharomyces cerevisiae and Penicillium commune. There was a significant difference (p<0.05) in gross energy and crude protein levels in all the fish samples. The fish samples showed high magnesium (>59.61mg/g) and potassium (>41.5661mg/g) levels whereas the iron content was low (<7.2361mg/g).