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Genetic differences within a 495 base pair section of the mitochondrial cytochrome b gene reveal a striking concordance among species in two monophyletic groups of Indo-west Pacific butterflyfishes. In both species groups, an approximately 2.0% genetic break clearly partitions individuals between the Indian Ocean and Pacific Ocean. However, levels of intra-Pacific mtDNA variation are low, on average less than 1.0%, and fail to cluster by species boundaries defined by colour pattern. Individuals from different species, separated by thousands of kilometers, often possess identical cytochrome b sequences, whereas conspecifics from the same reefs can show up to 1.5% difference. The discrepancy between the mtDNA gene tree and species boundaries may reflect retained ancestral variation or may be the result of hybridization. The strong temporal and phylogenetic concordance between these two independent …