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The most representative organisms of the Harbor of Gaeta Gulf in South Italy were analyzed for biofouling by visual census and confirmed later by molecular approach on an artificial Conatex panel dipped 3 m into a eutrophic area during the Covid-19 pandemic. Mitochondrial Cytochrome C oxidase subunit 1(COI) gene was sequenced from 20 different marine species (flora: 2 families, 2 orders; fauna: 16 families, 11 orders) to test whether the morphology-based assignment of the most common biofouling member was supported by DNA-based species identification. Twelve months of submersion resulted in generation of sufficient data to obtain a facies climax represented mainly by the bivalve mollusk, Mytilus galloprovincialis. Specific diversity and variations of the biofouling biomasses were analyzed using two different anti-biofouling paints: an endocrine disrupting chemical (EDC)-containing metal biocide, and a biocide-free paint. Also, their effects on detoxification and reproductive health of M. galloprovincialis were evaluated using glutathione S-transferase enzymatic activity and RTqPCR expression of the fertility antioxidant gene glutathione peroxidase 4 (gpx4). The obtained data provide useful indications on which future investigations may be focused and may become a potential management tool for a harbor biofouling database to assist local administrations in EDCs protection of autochthonous benthic communities and their fertility using innovative antifouling paints.