Biodiversity encompasses the variety of life at all complexity levels - from genes to ecosystems – and cannot therefore be described by species richness alone; consideration of functional diversity is also required. Marine ecosystems are undergoing biodiversity loss, making it fundamental to study their change over time. In the Mediterranean Sea, coralligenous reefs support biodiversity and complexity, but are affected by multiple stressors. This study investigates long-term changes in the Punta Mesco coralligenous reef (Ligurian Sea) by analysing quantitative cover data, collected since the 1960s at three depths: 20 m, 30 m and 40 m. Functional diversity (i.e., the variety of roles played by the species) and functional redundancy (i.e., the diversity of species playing a given role) were examined. To this purpose Biological Traits Analysis (BTA) was applied to assess whether changes in species composition had affected functionality. Species were characterised according to their biological traits associated with three main functions: trophism, three-dimensionality, and bioconstruction. Species were subsequently grouped into Functional Entities (FEs), defined as groups of species sharing the same combination of traits associated with the three functions considered. Results showed that the Punta Mesco coralligenous reefs underwent an abrupt shift between 1990 and 1996, and a further one between 2008 and 2017. The greatest changes occurred at 20 m depth, with a loss of functional diversity and a reduction in redundancy. At 30 m depth, functional diversity increased, but with FEs represented by a single species, which led to reduced redundancy. Coralligenous reef at 40 m exhibited some stability in functional diversity, but increased sedimentation reduced living cover. The changes over time in community composition and structure of the Punta Mesco coralligenous reef, already documented in previous studies, have therefore implied major alterations also in functional diversity and redundancy, thereby increasing ecosystem vulnerability.