PCR based nuclear and mitochondrial DNA markers are used to clarify cases of misidentification of adult individuals of fish species with morphological similarities. This problem prevails in the case of false scad (Caranx rhonchus) overlap geographically and has similar morphology with Turkish species of the genus Trachurus. Hence, the nuclear DNA/mitochondrial DNA approach was used for C. rhonchus, to identify and discriminate, it from Trachurus sp. coexist. Polymerase Chain Reaction (PCR) amplification of the nuclear 5S rDNA gene is a suitable method for differentiating between C. rhonchus and Trachurus sp. On the other hand, a PCR-RFLP technique, which involves digesting of the whole mitochondrial cytochrome b gene with XcmI and BsrGI restriction enzymes to generate DNA profiles, was used to identify of C rhonchus and discriminate it from three Trachurus sp. This PCR-RFLP analysis is simple, rapid and reliable and hence can be regularly used to discover fraudulent substitution among economically important C. rhonchus and Trachurus sp. Results have confirmed the usefulness of these techniques to distinguish and genetically identification of morphologically similar carangid species.