Mediterranean fish species living along Italian (Gaeta) and Egyptian (Alexandria) coasts were analyzed using DNA barcodes for molecular identification. Mitochondrial Cytochrome c Oxidase subunit 1 (COI) gene was sequenced from 31 different marine species to test whether the morphology-based assignment of individuals into 19 families, 6 orders was supported by DNA-based species delimitation and Neighbour Joining cladogram. All COI rRNA gene barcodes were matched with reference sequences of expected species, according to morphological identification. Neighbour joining tree was drawn based on COI rRNA gene and the majority of specimens clustered in agreement with their taxonomic classification. Our results updated Mediterranean edible fish knowledge providing graphical resources, taxonomical and bioinformatics references, improving the genetic fish database and the basic molecular information to strengthen the science–policy interface for biodiversity and ecosystem services as conservation, blue economy, and long-term human well-being.