Being repositories of ancient phyla as well as more recent specialized taxa, coral reefs are among the most spectacular, productive, diverse (per unit area), and threatened ecosystems on Earth. Organisms they house provide a critical source of protein for people in many tropical countries, and reefs themselves protect human populations from storm and wave damage. Coral reefs provide aesthetic beauty (and the bioeroded sand on beaches) for tourism—an increasingly important economic resource for developing tropical countries. However, tourism and other uses of reefs must be carefully managed to be of sustainable economic benefit. A fundamental value of coral reefs is that they provide an aesthetic, intellectual, educational, and cultural heritage for present and future generations.

Threats to global coral reefs, however, are severe and well documented (Bryant et al., 1998; Burke et al., 2002; Gardner et al., 2003; Hughes et al., 2003; Pandolfi et al., 2003, 2005; Bellwood et al., 2004; Burke and Maidens, 2004; Hoegh-Guldberg et al., 2007). Overexploitation has been identified as an especially serious problem, but other threats include coastal development and sedimentation, pollution, global warming, disease, and ocean acidification. The Global Coral Reef Monitoring Network reports that 20% of global coral reefs already have been degraded beyond recovery, an additional 24% are under imminent threat of collapse, and a further 26% are at longer-term risk (Wilkinson, 2004). In the Indo-West Pacific (IWP), 88% of Southeast Asian reefs and 61% and 54% of Middle Eastern and Indian Ocean (IO) reefs are at medium to high risk (Bryant et al., 1998; Burke et al., 2002). Human population density near reefs is particularly high in Southeast Asia and the IO. Pacific reefs are in better condition (59% at low risk), with more protected area, than those in other regions.

Despite the biological, cultural, and economic value of coral reefs and the widely publicized alarm at their global decline, it remains astonishing how little we know about the patterns of diversity (“diversity” will be used equivalently to species richness) on coral reefs that would help us manage and conserve them. This chapter will (i) review and provide new information on the geography of coral reef diversity in the IWP using information from the most ecologically important and well-known groups of reef organisms, (ii) provide a brief overview of the major factors that