The present study aims to evaluate if invasion of Caulerpa racemosa var. cylindracea can affect both alpha and beta diversity in Mediterranean coastal system. The following hypotheses were tested: (i) measures of alpha diversity differ between invaded and non-invaded assemblages (ii) this pattern is consistent between different habitats, (iii) assemblages from habitats which are naturally very different tend to be more similar when invaded compared to non-invaded situations. Results showed that Mediterranean benthic assemblages invaded by C. racemosa var. cylindracea were characterized by lower values of alpha diversity than non-invaded assemblages; moreover, differences between deep (25m) and shallow water (5m) assemblages appeared lower in invaded than in non-invaded areas, with a decrease of beta diversity. This homogenisation of habitats was related to a lack of several characteristic species and to a higher abundance of few opportunistic species in invaded areas, particularly turf-forming algae. Moreover, variability in taxa composition was lower in invaded than in non-invaded assemblages in both habitats.