Cross-community congruence patterns of species diversity metrics and community similarity between macrobenthic infauna, epibenthic megafauna, demersal fish and microzooplankton ciliates were studied in 6 areas in the Eastern Mediterranean. These species-rich communities, co-occurring in space and time, were intensively sampled during 2 cruises, in seasons reflecting different levels of subtle anthropogenic stress. Comparisons of patterns showed high positive correlation of similarities in community structure between macrofauna and megafauna, megafauna and fish and fish and microzooplankton. However, the employed diversity metrics varied between communities, occasionally showing negative correlations. We suggest that the species composition and diversity of these communities reflect different environmental gradients and sources of heterogeneity, and therefore none of them can be used as a surrogate for ecosystem biodiversity in the context of marine conservation planning