Climate emergency and other anthropogenic pressures urgently call for technological and methodological advances to enhance our ability to protect marine habitats and their ecosystem services. In recent years, environmental DNA (eDNA) metabarcoding has emerged as a powerful tool to achieve an integrative assessment of the environmental health status, through a broad, relatively rapid, and cost-effective taxonomic monitoring of biodiversity at different spatial scales. Here we provide a time-based overview of the applications of the eDNA metabarcoding methodology carried out across diverse Italian marine and coastal habitats, with an in-depth scrutiny of the commonly adopted operative procedures, from sampling to sequencing. The lack of standardization and low replicability in space/time arose as major issues of several monitoring campaigns, preventing appropriate cross-comparability of previous studies. Given the wide potential of eDNA metabarcoding surveys along the Italian coastline, this review aims to boost a wider application of eDNA metabarcoding for biodiversity inventories and to avoid major methodological weaknesses that could compromise the long-term value and broad spatial scope of future monitoring plans.
