1. Although it is widely recognized that protection may enhance size, abundance, and diversity of fish, its effect on spatial heterogeneity of fish assemblages and species turnover is still poorly understood. 2.Here the effect of full protection within a Mediterranean marine protected area on β-diversity patterns of fish assemblages along a depth gradient comparing a no-take zone with multiple unprotected areas is explored. The no-take zone showed significantly higher synecological parameters, higher β-diversity among depths, and lower small-scale heterogeneity of fish assemblages relative to unprotected areas.3. Such patterns might likely depend on the high level of fishing pressure outside the no-take zone, as also abundance-biomass curves seemed to indicate. Results suggested that full protection could play a role in maintaining high β-diversity, thus reducing the fragility of marine communities and ecosystems, and spatial heterogeneity may represent a reliable predictor of how management actions could provide insurance against undesirable phase shifts.