Molecular markers were used as indicators in assessing the genetic diversity of fish. They allow direct observation of genetic information and estimation of genetic relationships between the population and species. In the present study, five SCoT primers and five ISSR primers were used to estimate the genetic diversity. Fifteen samples of sand smelt fish species (three replicates for each species) were used in the present investigation. Sand smelt fish were collected from five different locations: (Fayoum, Burullus, Suez, Idiko and Port Said). The total number of DNA bands generated by ten primers 139 with an average of 13.9 amplicons /primer. The highest number of amplicon was 17 generated by ISSR-04 and the lowest number was 10 generated by SCoT-03. The total number of polymorphic amplicons was 63 with an average 6.3 / primer. The polymorphic amplicons ranged from 3 to 13 amplicons. Therefore, the ten primers expressed different levels of polymorphism, ranging from 20% with the primer ISSR _{- 2} to 81 % with the primer ISSR _-01. The frequency varied from 0.5 to 0.9 values where primer ISSR_-1 had the lowest frequency while primers ISSR_-02 and ISSR_-4 had the highest value with average 0.74. The polymorphic information content (PIC) varied from 0.24 to 0.37 values where primer ISSR_-03 had the lowest PIC value while primer ISSR_-01 had the highest value with average 0.32.