The advent of molecular tools such as Polymerase Chain Reaction (PCR) and Environmental DNA (eDNA) metabarcoding has significantly enhanced our ability to assess and monitor diverse ecosystems. eDNA metabarcoding, combined with High Throughput Sequencing (HTS), involves the analysis of genetic material dispersed in the environment, enabling its extensive sequencing. This technique offers a powerful and complementary approach to traditional species identification methods, including taxonomic identification and barcoding. It is particularly important in marine environments, where sampling and taxonomic analysis often requires considerable time and specialized expertise. This review provides an overview of key metabarcoding studies conducted in the Apulian region (southeastern Italy), aiming to offer a state-of-the-art background useful for future research. The Apulian region, rich in biodiversity, contains many ecologically and commercially significant habitats and species, some of which are endangered. Molecular studies, therefore, could represent a turning point in the routine assessment and management of these habitats. All the scientific papers in which metabarcoding techniques have been successfully applied in Apulia were summarized and discussed. Despite the region’s 1,040 km of coastline, the marine environment remains poorly investigated using these molecular approaches, highlighting a crucial priority for future research. Finally, this review serves as baseline knowledge critical for planning future eDNA metabarcoding studies and as a foundation for optimizing protocols and procedures to standardize workflows. By identifying current limitations and emphasizing key strengths, this work supports the development of robust experimental designs, ensuring that future results will effectively contribute to the management and protection of natural environments.

 

Key words: Biomonitoring, ecosystem disturbance, environmental DNA, environmental protection, marine ecology, Mediterranean Sea.