In the present study, the start codon targeted (SCoT) technique was used for measuring the genetic variability between two fish species of family Moronidae (Dicentrarchus punctus and Dicentrarchus labrax), these species were collected from the Mediterranean Sea, Port Said, Egypt. Eleven SCoT primers were used in the study of generating different lengths of amplicons that ranged from 150bp to 1800bp (SCoT-2, SCoT-3, SCoT-4, SCoT-6, SCoT-7, SCoT-8, SCoT-9, SCoT-10, SCoT-28, SCoT-35 and SCoT-46). The polymorphism percent ranged from 18% with SCOT-28 primer to 75% with SCOT-6. The genetic similarity between the two species was 75.5%. Protein analysis using Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was also performed in this study producing a total of 22 bands that ranged in size from 19KD to 200KD. Each of the two species produced 22 bands.