Molecular markers were used as indicators in assessing the genetic diversity of a fish, they allow for direct observation of genetic information and estimation of genetic relationships between the population and species. In the present study, eleven  SCoT primers and ten ISSR primers were used to estimate the genetic diversity among the four mullet species namely Mugil cephalus, Liza ramada, Liza grana, and Valamugil seheli collected from four different  Egypt governorates Alexandria, Ismailia, Port Said and Damietta. The two markers  SCoT and ISSR successfully amplified amplicons with a total number of 176 and 132 of which 153 and 111 were polymorphic, representing a percentage of polymorphism of 86.9% and 84.1% polymorphic amplicons/ primer, respectively. The similarity indices ranged from 0.47 to 0.84, 054 to 0.92   and 0.52 to 0.86  for SCoT, ISSR and combined, respectively. Cluster analysis based on similarity matrices of SCoT, ISSR and combined dendrograms revealed some similarities; for example, the grouping of the Mugile cephallus (Alexandria, Ismailia and Port Said) together and the grouping Valamugil seheli (Ismailia and Damietta)  based on the three dendrograms. Also, Liza ramada, Liza garana (Damietta) and Mugile cephallus ( Damietta) were clustered together based on the three dendrograms. From gene sequencing and NCBI Blast analysis identified of gene location in fish genomes. The NCBI blast tool was used to align our gene with the NCBI database and it revealed that this sequence is highly similar to a sequence located on fish species called Dicentrarchus labrax (the European bass). Also, the sequence is located on Chr1 near a gene called “Type II keratin E3".