The production of fishery products in the city of Sorong, was recorded at 44,710 tons in 2017, one of which was smoked skipjack tuna. The smoking of fish is done through the process of salting, and providing smoke. The purpose of smoking is to prevent damage to fish due to the process of decreasing water content. The unique characteristics of smoked fish are caused by the presence of volatile compounds that are easily vaporized and trapped in the fish flesh. The smoking process in fish affects the physical, chemical, microbiological and organoleptic properties of the product. The objective of this study was to determine the microbiological quality of smoked fish and to identify bacteria molecularly in smoked skipjack tuna in the market. The method used in this study is a descriptive method to describe the total plate count of microbes, examination of E. coli and Salmonella, as well as molecular identification of bacteria found in smoked skipjack tuna in market. The results showed that all samples indicated the presence of microbial TPC, examination results of E. coli and Salmonella were declared not to exceed the maximum limit according to Indonesian national standards. As for molecular identification, it was found that sample Ca.1 was identified as Bacillus thuringiensis BD17-E12, sample Ca.2 was identified as Bacillus cereus MD152, and sample Ca.3 was identified as Bacillus thuringiensis ucsc27.