Simple SummaryAn increasing number of different habitats leads to an increasing number of species and has been considered a key driver for biodiversity. However, there is no common understanding on how to measure habitat diversity. In this study, we tested a newly proposed measure of substrate heterogeneity by classifying changes on the seafloor with underwater video imaging. This analysis showed that the presence of small patches of different soft sediment types was associated with elevated species richness and a higher rate of occurrence of rare species.AbstractMany studies show that habitat complexity or habitat diversity plays a major role in biodiversity throughout different spatial scales: as structural heterogeneity increases, so does the number of available (micro-) habitats for the potential species inventory. The capability of housing species (even rare species) increases rapidly with increasing habitat heterogeneity. However, habitat complexity is not easy to measure in marine sublittoral sediments. In our study, we came up with a proposal to estimate sublittoral benthic habitat complexity using standard underwater video techniques. This tool was subsequently used to investigate the effect of habitat complexity on species richness in comparison to other environmental parameters in a marine protected area situated in the Fehmarn Belt, a narrow strait in the southwestern Baltic Sea. Our results show that species richness is significantly higher in heterogeneous substrates throughout all considered sediment types. Congruently, the presence of rare species increases with structural complexity. Our findings highlight the importance of the availability of microhabitats for benthic biodiversity as well as of the study area for regional ecosystem functioning.