Beds of Modiolus modiolus, in areas of moderate to strong tidal currents, develop into reefs with a relief of wave like undulations 0.09–0.45 m in amplitude and length scales of 6–18 m. Cores taken by diver operated suction sampler were targeted at positions on the ridges and troughs of a reef, in the Irish Sea off north-west Wales, allowing the fauna to be compared between adjoining ridges and troughs. Sessile epifauna was mostly attached to the larger mussels clumped together on the ridges. The crevice fauna and infauna were also nearly three times more abundant on the ridges, but the lists of species were similar from the two sub-habitats. Species richness was higher on the ridges, however, diversity and evenness measures were similar for ridges and trough samples. The Modiolus sub-habitats were found to be distinct from other macrofaunal assemblages in the wider southern Irish Sea. Deposition of faecal pellets in the spatially complex habitat amongst the mussels provided conditions suitable for an infauna more typical of inshore muddy sands enriched by organic matter. The scale of the ridge and trough morphology may increase variability between replicates when grabs are used remotely to sample this type of biogenic feature.