Despite important implications for theoretical ecology and conservation biology, the empirical relationship between β-diversity and community stability remains equivocal. For example, β-diversity (the rate of species spatial turnover) underlies most conservation strategies that aim to include the most species in a restricted number of sites. However, whether maximizing β-diversity also maximizes the temporal stability of biological communities, a key predictor of extinction risk, remains largely untested. We compared the spatial and temporal dissimilarity of fish communities inhabiting the largest coral reef ecosystem on Earth, the Great Barrier Reef of Australia. Fish β-diversity, measured as spatial turnover in species composition, and temporal stability (inverse of turnover) of communities were inversely related indicating that high β-diversity was associated with greater temporal stability, and thus, lower extinction risk. Our results demonstrated a strong β-diversity-stability relationship when all taxa were combined. While β-diversity tended to be associated with greater temporal stability at the community level, for one taxon, surgeonfishes (Acanthuridae, one of the most abundant reef fish families), this relationship was reversed. Therefore, the same β-diversity-stability relationship cannot be indiscriminately assumed for all taxa. We detected no effects of extrinsic factors (latitude, α-diversity, or dispersal-related characteristics such as reef area and isolation) on these relationships between spatial versus temporal turnover. We conclude therefore that conservation strategies reliant on β-diversity will need to consider biotic factors such as taxon identity, and possibly functional group membership, to ensure the effectiveness of protection measures.