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Marine habitats are often used as surrogates of biodiversity for Marine Park planning. In this study we investigate the significance of both habitat and wind exposure to reef-top macroinvertebrates to determine whether habitats alone provide a surrogate of biodiversity. Detailed habitat maps of the reef flat of Rarotonga (Cook Islands) and historical wind data, were used to assess the distribution and abundance of the macroinvertebrate fauna of the reef-top. Macroinvertebrates were surveyed along transects at 128 sites in four main, broad habitat types (rubble/rock, sand/ coral, sand and algal rim) and two exposure categories (windward/leeward). Analyses of variance on the most abundant species and multivariate ordination (nMDS) found that habitat was more important than exposure per se in explaining the abundance of species and the composition of assemblages. The rubble/rock habitat had the greatest substratum heterogeneity and structural complexity and supported the largest number of species and individuals. Five of the abundant holothurian species and two echinoids (Echinometra mathaei and Tripneustes gratilla) were most abundant in the rubble/rock, while two holothurian species (Holothuria cinerascens and Actinopyga mauritiana) and the gastropod Trochus niloticus, were most abundant in the algal rim. Spatial data for the five most abundant species and two of the key fisheries species highlighted the significance of the south-eastern, windward coast to all species, an area that is most likely to be impacted by an increase in the frequency and magnitude of major storm events under future climate change scenarios. [ABSTRACT FROM AUTHOR]