Whereas it is well known that ecosystem engineers can have a large influence on biodiversity, underlying mechanisms are still not fully clear. We try to enhance insight by comparing biodiversity effects of two neighboring intertidal, clonal, ecosystem engineering plant species that modify the physical environmental parameters in a similar way, but with a different magnitude. Macrobenthic assemblages were compared between meadows of the seagrass Zostera noltii, small patches (≤0.5 m Ø) and large areas (≫5 m Ø) of the emergent halophyte Spartina anglica and the surrounding bare tidal mudflat (control). Multivariate analyses revealed that the mudflat benthic assemblage and Zostera meadow assemblage showed highest similarities, whereas the Spartina marsh assemblage showed the highest dissimilarity with these two areas. Whereas the descriptive nature of our study limits interpretation of the data, some clear patterns were observed. For all vegetated areas, species diversity was lower compared to the unvegetated mudflat, and we observed a strong shift from endo- towards epibenthic species, suggesting that increased above-ground habitat complexity may be a main driving process in our system. As there were no clear patterns related to feeding types, food availability/productivity appeared to be of minor importance in structuring the benthic assemblages. Nevertheless, animals were in general smaller in vegetated areas. Patchiness had a distinct positive effect on biodiversity.