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Fish monitoring is essential for assessing the effects of natural and anthropic stressors on marine ecosystems. In this context, environmental DNA (eDNA) metabarcoding appears to be a promising tool, due to its efficiency in species detection. However, before this method can be fully implemented in monitoring programs, more studies are needed to evaluate its ability to assess the composition of fish assemblages compared with traditional survey methods that have been used for decades. Here, we used both eDNA metabarcoding and Underwater Visual Census (UVC) to assess the taxonomic and functional diversity (presence-absence data) of Mediterranean fish communities. We collected eDNA samples and performed UVC strip transects inside and outside four Marine Protected Areas in the Mediterranean Sea. Samples for eDNA analysis were collected by filtering seawater simultaneously at the surface and the bottom, and DNA was amplified using a combination of three sets of primers. We found that eDNA alone made an outstanding characterisation of fish composition with the detection of 95 % of the 60 taxa identified in this study, whereas UVC recovered only 58 % of them. Functional diversity was better evaluated with eDNA than with UVC, with the detection of a greater breadth of functional traits. eDNA was even better at characterising functional than taxonomic diversity, providing reliable information on ecosystem functioning with little sampling effort. Together these results suggest that eDNA metabarcoding offers great potential for surveying complex marine ecosystems. Combining eDNA metabarcoding and UVC in integrated monitoring programs would therefore improve monitoring strategies and enhance our understanding of fish communities, a key step promoting their conservation., (Copyright © 2024. Published by Elsevier B.V.)