Abstract This paper aims at providing a standardized procedure to assess the ecological quality of Mediterranean marine habitats in relation to biological invasions by macroalgae through the employment of the ALEX index. Available data from previous ALEX applications were used to optimize the sampling design and to propose a standardized procedure. The procedure was applied to the main Mediterranean sensitive habitats, coralligenous reefs and meadows of the endemic seagrass Posidonia oceanica, at two sites in the north‐western Mediterranean Sea. A total of 73 native macroalgal taxa and four introduced taxa (the Chlorophyta Caulerpa cylindracea and the turf forming Rhodophyta Acrothamnion preissii, Womersleyella setacea and Asparagopsis spp.) were identified. Coralligenous reefs exhibited a higher abundance of both C. cylindracea and introduced turf species, while P. oceanica meadows were mostly affected by W. setacea and A. preissii. The application of ALEX for different years on coralligenous reefs highlighted the consistency of the index over time in the absence of further invasions. The use of ALEX index with other ecological quality indices showed similar patterns in both habitats. The concurrent assessment of the ecological quality of ecosystems by generic indices and the level of invasion through ALEX index may be a useful approach for answer to requirements of the European Directives and to plan even more complete and effective conservation programmes.
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