Species of family Sparidae, commonly called, sea breams, are widely distributed from temperate to tropical waters and are of great economic interest. However, in Egypt, limited data is available on genetic variation and evolutionary relationships of family Sparidae. Therefore, the study of the genetic diversity among sparid species is crucial for proper management and convenient strategies. The aim of this study was to evaluate the genetic diversification among 22 species belonging to family Sparidae from the Mediterranean Sea and the Red Sea in Egypt using three different molecular markers. DNA barcoding, using Cyt-b mitochondrial gene, was applied as an initial step for species identification and diversification. In addition, Randomly Amplified Polymorphic DNA (RAPD), and Inter Simple Sequence Repeat (ISSR) markers were employed in estimating the genetic diversity among the studied species.  Based on each molecular marker, a phylogenetic tree was constructed for the studied sparid species according to the calculated genetic distance/ similarity. DNA barcoding using mitochondrial Cyt-b gene provided efficient DNA barcodes for most of the studied species. RAPD assays (using 20 RAPD primers) produced a total of 308 bands, of which 91.8% were polymorphic. Eight ISSR primers amplified a total of 197 bands, 97.9% of which were polymorphic. RAPD and ISSR profiles differed substantially among the 22 sparid species, enabling easy discrimination. However, ISSR had a higher power of discrimination compared to RAPD markers. The constructed phylogenetic trees based on the employed molecular markers provided the update for the barcoded Sparidae species evolution. The employed molecular markers in this study were efficient in species genetic diversification. Cyt-b was successfully utilized in species barcoding, whereas, the combination of RAPD and ISSR-PCR profiles provided substantially differentiated profiles for each species, which makes them suitable for measuring genetic divergence among species.