A total of 30 microbialites at two sites in Lake Clifton, Yalgorup National Park, Western Australia, were sampled by coring to quantify the associated fauna with these organo-sedimentary structures. Twenty five species of aquatic fauna were recorded from the cores, comprising 20 species of metazoan, predominantly Crustacea (including Melita kauerti (Amphipoda), Exophaeroma cf. serventii (Isopoda); and Cyprideis australiensis (Ostracoda); Polychaeta (Capitella cf. capitata); nematodes and five species of Foraminifera (Protista). Multivariate analysis of the five numerically most abundant taxa (amphipods, isopods. ostracods, polychaetes., nematodes) separated microbialites by season and submergence. Numbers of all taxa, particularly polychaetes and amphipods, were much higher in spring than in autumn, and in permanently-inundated than in seasonally-inundated microbialites. The exception was higher numbers of juvenile polychaetes in seasonally-inundated microbialites at the northern site in spring, This study showed that modern thrombolitic microbialites can co-exist with a diverse invertebrate fauna and serves as a baseline for future studies of interactions between microbialites and fauna.