Cold seeps are among the most heterogeneous of all continental margin habitats. Abiotic sources of heterogeneity in these systems include local variability in fluid flow, geochemistry, and substrate type, which give rise to different sets of microbial communities, microbial symbiont-bearing foundation species, and associated heterotrophic species. Biogenic habitats created by microbial mats and the symbiotic species including vesicomyid clams, bathymodiolin mussels, and siboglinid tubeworms add an additional layer of complexity to seep habitats. These forms of habitat heterogeneity result in a variety of macrofaunal and meiofaunal communities that respond to changes in structural complexity, habitat geochemistry, nutrient sources, and interspecific interactions in different ways and at different scales. These responses are predicted by a set of theoretical metacommunity models, the most appropriate of which for seep systems appears to be the ‘species sorting’ concept, an extension of niche theory. This concept is demonstrated through predictable patterns of community assembly, succession, and beta-level diversity. These processes are described using a newly developed analytical technique examining the change in the slope of the species accumulation curve with the number of habitats examined. The diversity response to heterogeneity has a consistent form, but quantitatively changes at different seep sites around the world as the types of habitats present and the size-classes of fauna analyzed change. The increase in beta diversity across seep habitat types demonstrates that cold seeps and associated biogenic habitats are significant sources of heterogeneity on continental margins globally.