Biodiversity encompasses a range of different levels of organization from the genetic variation between individuals and populations to species diversity, assemblages, habitats, landscapes, and biogeographical provinces (Gray 2000). Whittaker (1960) suggested that there was a range in scales of species richness and partitioned diversity into alpha, beta, gamma, and epsilon components to characterize different aspects of diversity in relation to spatial scale. Alpha diversity is the diversity within a single habitat, beta diversity measures the degree of change in the composition of samples along gradient or the extent of the difference in samples from the opposite end of a gradient (Gray 2000), and gamma diversity is the diversity within homogeneous sampling units (i.e., region, including different habitats), and epsilon diversity is the total diversity within a region (Gray 2000). The knowledge of the processes that determine patterns of species diversity in space and time is a major focus of ecological research (Ricklefs and Schluter 1993). Several factors can be invoked to explain the spatial patterns of biodiversity: historical, phylogenetic, and climate processes are important determinants of regional pools of species (i.e., gamma diversity), whereas biotic interactions play a key role in determining local diversity (i.e., alpha diversity). Changes in the physical characteristics of the habitat can strongly affect variation in composition and abundance of species among sites, thus inuencing beta diversity (Danovaro et al. 2004, 2008a; Balata et al. 2007; Pusceddu et al. 2008). Biodiversity can also be measured in terms of functional traits as well as the functional role and identity of the species reported in the investigated areas (Cardinale et al. 2006). Here we report the most common diversity indices to measure benthic structural and functional diversity.