Submarine caves are considered as a top priority for conservation, but the effects of common pressures are poorly known for these habitats. Here, we examined the effect of recreational human visitation on a selection of submarine caves in a Mediterranean Marine Protected Area (403504000N; 81103900E) where diving activities are regulated. Sampling was conducted in visited and not visited caves to assess whether diving activities have a significant effect on cave habitats, what are the components of biodiversity most affected by this disturbance, and its potential effects on spatial heterogeneity of benthic assemblages. Results clearly showed that human visitation could significantly affect spatial patterns of benthic assemblages. Organisms with erect growth forms were significantly more abundant and homogeneously distributed where diving activities are forbidden. An increase in the small-scale heterogeneity of assemblages and a decrease in their threedimensional structure could be the ultimate consequences of human visitation. The interaction between specific stressors and the patterns of distribution of species and assemblages can drive their spatial heterogeneity also in unique habitats like marine caves, representing an early warning for the development of appropriate management measures.