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Abstract Aim We analysed data on Indo-Pacific coral reef taxa to test four mechanisms proposed for the origins of the biodiversity centre in the East Indies Triangle: (1) the centre of origin hypothesis, (2) the centre of accumulation hypothesis, (3) the centre of overlap hypothesis, and (4) the bioaccumulation hypothesis. Location The Indian and western Pacific oceans. Methods The data set consisted of eight clades of fishes, four of corals and one of molluscs, consisting of a total of 95 species, with 72 informative nodes, in 29 areas. We used phylogenetic analysis for comparing trees (PACT) to reconstruct reticulate area relationships. Results An analysis using PACT produced very little congruence between area relationships among the histories of the taxa examined. Only two sets of two taxa each showed substantial congruence; several other taxa showed partial congruence. Main conclusions Despite numerous ‘explanatory’ claims for the incredible biodiversity of the marine macrofauna of the East Indies Triangle, the patterns obtained here did not accord with any of the hypotheses proposed. It is possible that, with the addition of more taxa, additional patterns would emerge. Much more systematic work within the East Indies is required to resolve this problem.