Haploops nirae is a gregarious tubiculous amphipod which extended its habitat over thousands of hectares in shallow waters of South Brittany bays (Bay of Biscay, Atlantic) over the last decades and created uniquely large and dense tube mats. In the bay of Concarneau, we investigated the specific diversity (i.e. species richness and species composition) and the functional structure (using biological traits) of the macrofauna associated with this Haploops community as a comparison with several surrounding soft-sediment communities to determine the effect of this engineer species on ecosystem functions. We showed that the occurrence of Haploops tubes and individuals significantly modifies sediment features (e.g. change in sediment grain size, increase in C and N organic content) but also largely affect species diversity and benthic composition. The species richness was significantly higher in Haploops community but the species assemblage associated with Haploops habitat was very homogeneous compared to the neighboring habitats and unique with 33% of all species exclusively found in this community. Multivariate analysis (dbRDA) revealed that Haploops density was by far the factor explaining the variation in species composition of benthic communities. No differences in species diversity and assemblage were detected in relationship to Haploops density. A biological trait analysis performed on the whole ecosystem (Haploops included) revealed that Haploops largely dominates the functional structure of the Haploops community by its own functional traits. When performed on selected traits of the associated fauna only (Haploops excluded) the functional structure of the Haploops community was characterized by a greatly reduced proportion of small to medium long lived, sensitive to disturbance, free living or burrowing/tube-building filter-feeding species. H. nirae appears to be a bioengineer and a foundation species that largely modifies its hydro-sedimentary features, controlling diversity and abundances of associated species, and creating a complex set of positive and negative interactions so that a unique benthic assemblage is found in sediments they colonized.