Bivalve molluscs are a diverse group of animals with particular economic and ecological importance. Their morphological characteristics frequently confuse their identification leading to mislabelling of edible species. Genetic diversity is critical to the resilience of marine bivalve populations in the face of environmental stressors such as ocean acidification and warming. In this study, we characterized the phylogeny and defined the first DNA barcodes of six marine bivalves [Ostrea edulis (Linnaeus, 1758) Arca noae (Linnaeus, 1758), Pinctada radiata (Leach, 1814), Venus verrucosa (Linnaeus, 1758), Calllista chione (Linnaeus, 1758) and Ruditapes decussatus (Linnaeus, 1758)] sampled from different coastal areas of Aegean and Ionian Seas using the molecular markers cytochrome c oxidase subunit I (COI) and 18S ribosomal RNA (18S rRNA). Further, COI gene was employed to investigate the population genetic diversity since 18S rRNA exhibited no conspecific differences. The sequence of 18S rRNA successfully discriminated the bivalves at family or superfamily level but occasionally proved insufficient for species identification. Contrariwise, COI was highly informative and could reliably distinguish all species. Population haplotype diversity was moderate to high and was always accompanied by generally low nucleotide diversity, indicating genetically closely related haplotypes. The invasive Pinctada radiata was found to be panmictic even among distant sampling areas, while Ostrea edulis was the only species that exhibited moderate levels of population subdivision. Finally, here we report for the first time the presence of Ostrea stentina in Thermaikos Gulf sampled among Ostrea edulis specimens, demonstrating a new invasive bivalve species in Eastern Mediterranean.