This paper continues our review of coral reef attributes and presents a research strategy for creating coral reef indexes of biotic integrity (IBI's) that, once developed, can be used in coral reef biocriteria programs and for the diagnostic monitoring of coral reefs around the world. A framework for the definition of coral reef multimetric indexes is provided and we demonstrate how existing research fits into this framework. The research strategy has 6 components; sessile epibenthos, benthic macroinvertebrates, fish, macrophytes, phytoplankton and zooplankton. The research strategy is based on our best judgement, other expert opinion, and available information. It draws on techniques that have been successful in freshwater, estuarine, and temperate marine biocriteria programs and outlines those that will likely be successful in coral reef environments.