Effective management of rocky intertidal reefs requires an understanding of spatial variation in species composition and abundance, and the identification of high biodiversity areas. This study identified patterns of invertebrate biodiversity on intertidal reefs of differing underlying structure within Ngari Capes Marine Park, south-west Western Australia. Intertidal reef surveys were conducted at 12 limestone and 9 granite sites throughout the park. Geology was a significant indicator of variation in percentage cover of substrate and invertebrate composition, which covaried with rugosity and complexity. Limestone reefs were characterised by a combination of high and low branching algae and a sand-turf matrix, whereas granite reefs consisted of bare rock. A total of 15 772 individual invertebrates representing 10 phyla, 16 classes, 60 families and 121 species was recorded. A high abundance of dove (Family Columbellidae) and jewel top snails (Family Trochidae) characterised limestone reefs, whereas an assortment of limpets and chitons characterised granite reefs. Granite reefs contained more species (92 v. 63) and a higher mean (+/- s.d.) number of individuals (119 +/- 58 v. 42 +/- 79 m(-2)) than did limestone reefs. These findings emphasise the effect of underlying geology on the distribution of intertidal invertebrates and the need for management programs to accommodate different habitat types to effectively conserve biodiversity.