The main goal of this study was to estimate genetic differences of samples of European Sea bass from three different locations (Red Sea, Mediterranean and Suez Canal). A total of sixty-four samples have been collected during the period from October to January… with average weight ranged from 250-300 gm. Morphometric traits such as fish weight, body length, tail length and others were measured. From the samples of each location, The DNA extracted individually using QIAGEIEN kit. Two biotechnology techniques have used [Restriction Fragment Length Polymorphism based on polymerase chain reaction (PCR-RFLP) and Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE (] to distinguish the genetic variants among the locations under the investigation. The morphometric traits show no significant differences between the samples from the three locations. The similarity matrix showed strong similarities between samples of Mediterranean Sea and the Suez Canal. Furthermore, samples from Red sea were more distinct from those of Mediterranean Sea and Suez Canal, although ecosystem of Red Sea and Mediterranean Sea are closely related, the similarity between them reached 55%; otherwise, it is 75% between samples of both Suez Canal and Mediterranean Sea. Furthermore, SDS-PAGE analysis in the samples of Suez Canal were genetically in close related to both of Mediterranean and Red Seas. In addition, heat map's results emphasize the obtained results. From the present study, both PCR-RFLP and the SDS-PAGE had proved to be exceedingly successful in distinguishing between samples under study and genetic assorted variety between them.