Tropical harmful algal blooms (HABs) are increasing in frequency and intensity and are substantially affecting marine communities. In October/November 2008 a large-scale HAB event (> 500 km2, dinoflagellate Cochlodinium polykrikoides) in the Gulf of Oman caused the complete loss of the branching corals, Pocillopora and Acropora spp., and substantial reductions in the abundance, richness and trophic diversity of the associated coral reef fish communities. Although the causative agents of this C. polykrikoides bloom are unknown, increased coastal enrichment, natural oceanographic mechanisms, and the recent expansion of this species within ballast water discharge are expected to be the main agents. With rapid changes in oceanic climate, enhanced coastal eutrophication and increased global distribution of HAB species within ballast water, large-scale HAB events are predicted to increase dramatically in both intensity and distribution and can be expected to have increasingly negative effects on coral reef communities globally.