The Pacific iguanas of the Fijian and Tongan archipelagos are a biogeographic enigma in that their closest relatives are found only in the New World. They currently comprise two genera and four species of extinct and extant taxa. The two extant species, Brachylophus fasciatus from Fiji, Tonga, and Vanuatu and Brachylophus vitiensis from western Fiji, are of considerable conservation concern with B. vitiensis listed as critically endangered. A recent molecular study has shown that Brachylophus comprised three evolutionarily significant units. To test these conclusions and to reevaluate the phylogenetic and biogeographic relationships within Brachylophus, we generated an mtDNA dataset consisting of 1462 base pairs for 61 individuals from 13 islands, representing both Brachylophus species. Unweighted parsimony analyses and Bayesian analyses produced a well-resolved phylogenetic hypothesis supported by high bootstrap values and posterior probabilities within Brachylophus. Our data reject the monophyly of specimens previously believed to comprise B. fasciatus. Instead, our data demonstrate that living Brachylophus comprise three robust and well-supported clades that do not correspond to current taxonomy. One of these clades comprises B. fasciatus from the Lau group of Fiji and Tonga (type locality for B. fasciatus), while a second comprises putative B. fasciatus from the central regions of Fiji, which we refer to here as B. n. sp. Animals in this clade form the sister group to B. vitiensis rather than other B. fasciatus. We herein describe this clade as a new species of Brachylophus based on molecular and morphological data. With only one exception, every island is home to one or more unique haplotypes. We discuss alternative biogeographic hypotheses to explain their distribution in the Pacific and the difficulties of distinguishing these. Together, our molecular and taxonomic results have important implications for future conservation initiatives for the Pacific iguanas. ?? 2008 The Royal Society.