In this dissertation, the biological and ecological characteristics of the two most important species in Mediterranean aquaculture are presented, for which a quality genome draft is available, gilthead sea bream Sparus aurata (Linnaeus, 1758) and European seabass Dicentrarchus labrax (Linnaeus, 1758). Gilthead sea bream is a protandrous species and an interesting model for the study of hermaphroditism and sex-biased (SB) genes development whose differential expression leads to the development of sexual dimorphism. The gilthead sea bream genome consists of 760 Mbp and 24 chromosomes in a haploid cell. It has been observed that sex-biased genes of gilthead sea bream behave differently than in gonochoristic species and that only highly conserved female sex-biased genes with a strong difference in expression evolve faster than non-biased genes. This fact is potentially linked to reduced effective size of the famle population and relaxed purifying selection. European seabass is a euryhaline species and several gene families with a role in osmoregulation and membrane transport (claudins, aquaporins, prolactins) have been identified in its genome. Seabass genome is slightly smaller than the glithead sea bream genome and also has 24 chromosomes. The analysis of nucleotide diversity at the whole-geome level revealed interesting heterogeneous patterns of differentiation and reduced recombination, possibly resulting from erosion of divergence and uneven introgression due to secondary contact after a long period of allopatric isolation.