The last decade has seen major advances in our understanding of the evolutionary history of fishes on coral reefs. Where molecular and morphological phylogenies often clashed, they are now largely concordant, revealing clear patterns in reef fish evolution. This chapter synthesizes recent morphological and molecular evidence to address the evolution of both the forms and functions of fishes on coral reefs. Recent evidence allows us to identify six clear phases in the co-evolution of fishes and reefs. Over the past 400 million years, interactions between fishes and reefs have intensified from initial indifference to the complex ecosystems we see today, where coral reefs are highly dependent upon fish assemblages. Coral reefs, in turn, have acted as both cradles and refuges for fish lineages, underpinning both increased diversity and reduced extinctions. However, modern reefs are in decline. In many cases, coral reefs are losing crucial functions which have been established for tens of millions of years. Our understanding of how reefs functioned in the past offers a unique insight into the potential future of coral reefs.

In an earlier review of the evolution of reef fishes in Sale [2237], Bellwood and Wainwright [194] suggested that “The combination of fossil evidence, molecular systematics, and vicariance biogeography offers an exciting avenue for future research.” In this, at least, they were right. The past decade has seen a series of spectacular advances in our understanding of the evolutionary history of reef fishes. With regional-and global-scale data sets, and new analytical approaches in both biogeography and molecular phylogenetics, we have finally begun to unravel the evolutionary history of reef fishes. This has enabled us to test some of the key hypotheses informing marine evolutionary and biogeographic theory. To explore the nature of these discoveries, and to place current findings in context, we will use a similar structure to the 2002 Sale chapter [194] to highlight how far our understanding has come.