The mussel Perumytilus purpuratus is distributed from Ecuador to the Strait of Magellan on the Pacific coast; and also extends along the Atlantic coast up to La Lobería, Argentina. The species forms dense three-dimensional matrices which constitute a microhabitat for a wide variety of organisms. Here we test the hypothesis that factors determining habitat structural complexity and environmental heterogeneity of Perumytilus matrices have significant effects on the associated macrofaunal community. In total we found 92 invertebrate taxa in P. purpuratus matrices. The number of layers (stratification) in the matrix had a significant effect on evenness: the greater the stratification, the lower the evenness index. Sediment retention by matrices in sheltered sectors had a significant effect on evenness: greater sediment retention resulted in lower evenness. Sediment retention also determined significant differences in macrofaunal assemblages. In matrices without sediment retention, mussel layering and the presence of algae on the shells of P. purpuratus determined significant macrofaunal differences. As a dominant competitor, P. purpuratus plays a major role in intertidal rocky shores where it is present, structuring communities and determining local biodiversity.