In this study, a combination of univariate and multivariate analysis was used to compare macroalgal assemblages of Mediterranean coralligenous system in areas invaded by the alien species Caulerpa racemosa var. cylindracea and Womersleyella setacea with reference assemblages. Results showed that assemblages strongly differed between invaded and reference areas in relation to both assemblage structure and species richness. Moreover, significant differences were detected between assemblages colonized by different invaders: C. racemosa var. cylindracea seemed to affect mostly encrusting organisms, while turf algae decreased in areas invaded by W. setacea. The present study showed that invasions of alien macroalgae could represent a serious threat for Mediterranean coralligenous assemblages.