The Random Amplified Polymorphic DNA (RAPD) technique offers an useful tool to investigate DNA polymorphisms. It can be used to distinguish different populations belong to one species. These markers also represent an efficient and inexpensive way to generate molecular data and thus, they have been used successfully in various taxonomic and phylogenetic studies. Information on the genetic structure of native fish populations is essential for studying molecular systematics and optimising fisheries management. RAPD assay was evaluated for studying genetic relationships and diversed in eight populations of whiting (Family: Gadidae). We used RAPD to determine the genetic characterization and the stock differentiation of whiting, Merlangius merlangus euxinus, eigth populations in the Black Sea coast of Turkey by using eleven arbitrary primers. The genetic relationship among the determined eight stations was estimated according to Jaccard similarity index and cluster analysis. Jaccard similarity coefficient values ranged from 0.676 to 0.836. The lowest similarity (0.676) was found between Karasu ve Rize and the highest similarity (0.836) was between Kiyikoy ve Zonguldak. In consequence of cluster analysis, two stations were classified in the first branch of the derived dendogram while the others were classified in the second branch. The average similarity between the two branches was 0.720. Among the primers tested, OPAB-01, 08, 14, 17, OPA-08, 12, 19, OPB-08 and OPC-11 showed polymorphic bands. Amplified fragments ranged from 218 to 2196 base pairs and the numbers of bands for each primer varied from 2 to 9.