Throughout the Pacific, many species of echinoderms and molluscs have cultural value and are harvested extensively in subsistence fisheries. Many of these species are sedentary and often associated with distinct reef-top habitats. Despite the significance of reef habitats and their fauna for fisheries and biodiversity etc, little information has been available on the distribution of habitats and their influence on the reef-top fauna in the Cook Islands. This thesis developed a novel approach to assess the status of the shallow-water reef-tops of Rarotonga, Cook Islands, to provide critical information to fisheries and conservation managers. The approach used remote sensing (aerial photography with ground truthing) to map the spatial arrangement and extent of the entire reef-top habitats accurately, and historical wind data and coastline shape to determine the windward and leeward sides of the island. The benthic habitat maps and degree of wind exposure were used to design and undertake a stratified sampling programme to assess the distribution and abundance of the epibenthic macroinvertebrate fauna of the reef-top. I quantified the distribution and abundance of the epibenthic macroinvertebrates and how they varied with habitat, assessed the effectiveness of a traditional ra'ui (marine protected area) for conserving stocks of Trochus niloticus and other invertebrates, and investigated the reproductive biology and impacts of traditional gonad harvesting on Holothuria leucospilota.