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European Union food legislation is dominated by particularly strict restrictions for edible products of animal and plant origin. Furthermore, traditional specialties are protected and promoted and geographical indications are applied to ensure that specific quality foodstuffs and agricultural products are genuinely originating from a specific region. These protection schemes are usually referred as PGI (Protected Geographical Indication), PDO (Protected Designation of Origin) or even TSG (Traditional Specialties Guaranteed) and guarantee the origin of these products. In the context of this dissertation, the issue of identifying innovative protected geographical indication products (PGIs) of specific species of the Amvrakikos Gulf with the use of DNA methodologies was studied. In particular two mitochondrial genetic markers, the COI and Cytb genes were used. 60 samples of the species Mullus barbatus were collected from three areas: the bay of Kalloni, the Ionian Sea and the Amvrakikos Gulf (20 samples per population). Isolation of DNA, agarose gel electrophoresis, amplification of the two genes by the PCR method and electrophoresis of their products on agarose gel were performed. Finally, the PCR products were purified and sequenced in the ABI 3500 automated analyzer. After the haplotypes were found for each gene and in each population, phylogenetic trees of the haplotypes were constructed. Also, the genetic distances between the populations for each gene and for the whole sequences were calculated. The corresponding phylogenetic trees of the studied populations were then constructed with the help of the appropriate statistical software. Finally, the value of the FST among populations was calculated to assess their genetic differentiation. Based on the statistical analysis of the results (estimation of genetic distances, construction of phylogenetic trees of the populations, FST index values) it seems that the population of the Ionian Sea is significantly differentiated from that of Kalloni Bay. Furthermore, there is no significant differentiation among the other populations. The findings of the present study, if enriched with: more mitochondrial DNA data, sampling from other areas of the Ionian Sea and combined with other biochemical, environmental and folklore studies, can clarify the field of genetic heterogeneity from these regions and eventually to contribute to the registration of Mullus barbatus from the Ionian Sea as a PDO - PGI product.