Résumé
Rhodolith beds, recognized as biodiversity hotspots with high ecological and conservation importance, face local anthropic pressures, including trawl fishing. However, monitoring the diversity associated with this sensitive biogenic habitat in the deep waters of the Mediterranean Sea is challenging. Traditional monitoring methods, such as experimental trawling and trammel nets, are extractive and have sampling limitations in providing comprehensive diversity inventories. In this work, we explore three alternative techniques (still video cameras, environmental DNA [eDNA] and bioacoustics) to monitor fish assemblages associated with rhodolith beds in the Menorca Channel at 45–80 m depth. Ten sites were surveyed with eDNA, and 66 fish taxa were identified, including endangered sharks and cryptic species. The molecular operational taxonomic units (MOTUs) richness varied significantly according to habitat heterogeneity, being higher in homogeneous bottoms, and to exposure to trawling, with higher richness in non‐exposed areas. Bioacoustics, though limited by a reduced library of fish sounds, detected differences in sound richness between habitat types, and the highest abundance of sounds was recorded in the areas with the greatest small‐scale habitat heterogeneity. Underwater video revealed limitations in species detection but proved effective for characterizing small‐scale habitat types and heterogeneity. In summary, each technique provides valuable information at different spatial scales and levels of detail. To assess the feasibility of these techniques for long‐term monitoring, we explored their capabilities and limitations in terms of costs, survey logistics and data output.