Background: The fish family Haemulidae is divided in two subfamilies, Haemulinae and Plectorhynchinae (sweetlips), including approximately 17 genera and 145 species. The family has a broad geographic distribution that encompasses contrasting ecological habitats resulting in a unique potential for evolutionary hypotheses testing. In the present work we have examined the phylogenetic relationships of the family using selected representatives of additional Percomorpha based on Bayesian and Maximum likelihood methods by means of three mitochondrial genes. We also developed a phylogenetic hypothesis of the New World species based on five molecular markers (three mitochondrial and two nuclear) as a framework to evaluate the evolutionary history, the ecological diversification and speciation patterns of this group. Results: Mitochondrial genes and different reconstruction methods consistently recovered a monophyletic Haemulidae with the Sillaginidae as its sister clade (although with low support values). Previous studies proposed different relationships that were not recovered in this analysis. We also present a robust molecular phylogeny of Haemulinae based on the combined data of two nuclear and three mitochondrial genes. All topologies support the monophyly of both sub-families (Haemulinae, Plectorhinchinae). The genus Pomadasys was shown to be polyphyletic and Haemulon, Anisotremus, and Plectorhinchus were found to be paraphyletic. Four of seven presumed geminate pairs were indeed found to be sister species, however our data did not support a contemporaneous divergence. Analyses also revealed that differential use of habitat might have played an important role in the speciation dynamics of this group of fishes, in particular among New World species where extensive sample coverage was available. Conclusions: This study provides a new hypothesis for the sister clade of Hamulidae and a robust phylogeny of the latter. The presence of para- and polyphyletic genera underscores the need for a taxonomic reassessment within the family. A scarce sampling of the Old World Pomadasys species prevents us to definitively point to a New World origin of the sub-familiy Hamulinae, however our data suggest that this is likely to be the case. This study also illustrates how life history habitat influences speciation and evolutionary trajectories. © 2012 Tavera et al.