Coralligenous habitat is one of the most important coastal systems of the Mediterranean Sea. This paper evaluates the main threats to macroalgal coralligenous habitats through a review of the relevant literature. Sedimentation, nutrient enrichment and biological invasions can cause severe alterations in the structure of coralligenous assemblages due to the regression of perennial structuring species and increases in populations of ephemeral algae. Under pristine conditions, mechanical disturbance seems to be easily mitigated by the recovery capability of coralligenous assemblages; however, such disturbances seriously affect coralligenous structure if they occur in concert with other stressors. Important synergetic effects among all the studied anthropogenic disturbances are also highlighted. The main consequences of the considered stressors are the loss of the complexity of macroalgal assemblages and the deterioration of both alpha and beta diversity.