The role of habitat structure in controlling the composition of assemblages has often been studied, but is rarely manipulated so that it is distinguishable from other factors. Differences in habitat structure as determined by differences in mussel size structure may affect the diversity of assemblages associated with mussel beds. Previous studies examining the effect of the size of individual mussels in a patch on the diversity of associated macro-faunal assemblages confounded the age of the patch with the size of the mussels. We manipulated the age of mussel patches and the size of the mussels within them to test experimentally whether the size of mussels influenced the structure of associated assemblages. At one of the two locations considered, the structure of macro-faunal assemblages in patches of larger mussels differed significantly from those in patches of the same age composed of smaller mussels. At this location, the size of mussels did not affect species richness but the abundance and proportion of organisms present differed depending on the size of the mussels. Here patches of larger mussels contained greater numbers of Nematodes and Oligochaetes and a lower abundance of taxa such as Jaera forsmani and Lepidonotus clava. We also found that invertebrate assemblages in general differed between the two locations. The effect of the size structure of mussels, however, varied spatially demonstrating that the effect of habitat structure on the diversity of associated assemblages is context dependent.