Background/Objectives: Environmental DNA (eDNA) is increasingly recognised as a powerful molecular tool for biodiversity monitoring, enabling the detection of species through trace genetic material found in environmental samples. This study investigates the utility of eDNA analysis for identifying vertebrate marine species in the central Mediterranean, with a focus on taxa that serve as ecological indicators to local ecosystems. Methods: Seawater samples were collected from nine sites around the Maltese Islands between May and August 2021, at depths ranging from 2 to 5 m. Samples were filtered and DNA was extracted, amplified and sequenced. The resulting sequences were processed through a bioinformatics pipeline, clustered into molecular operational taxonomic units (MOTUs) and assigned taxonomic identities using reference databases. Results: This study led to the detection of 70 MOTUs, including ecologically important species such as the loggerhead turtle (Caretta caretta), the striped dolphin (Stenella coeruleoalba) and the bottlenose dolphin (Tursiops truncatus), underscoring the method’s effectiveness in the detection of taxa of conservation value. Additionally, we detected a number of overlooked Blenniidae and Gobiidae taxa and deep-water or rarely encountered species such as the ocean sunfish (Mola mola), Cornish blackfish (Schedophilus medusophagus), Haifa grouper (Hyporthodus haifensis) and Madeira lantern fish (Ceratoscopelus maderensis). eDNA of the invasive dusky spinefoot (Siganus luridus) and that of the lumpfish (Cyclopterus lumpus), a species not previously recorded in Maltese waters, was also detected during this study. The latter’s detection highlights the potential of this methodology as an early detection tool for biological invasions. Conclusions: These findings support the integration of eDNA surveillance into marine biodiversity monitoring frameworks, particularly within marine protected areas to monitor native indicator taxa and assess the effectiveness of conservation measures, but also in ports and bunkering zones, where the risk of alien species introduction is elevated, with potential subsequent invasive species expansion that impacts native species and habitats.
Vella et al. (2025) studied this question.