Boxfishes (superfamily Ostracioidea, order Tetraodontiformes) are comprised of 37 species within the families Aracanidae (13 sp.) and Ostracidae (24 sp.). These species are characterized by several dramatic reductive trends in their axial and appendicular skeleton, and by the presence of a carapace formed by enlarged and thickened scale plates. While strong support exists for the monophyly of both families, interspecific relationships remain unclear as no species-level molecular phylogeny currently exists for either of these two clades, and the only hypotheses of relationships are based on morphological studies that were mostly restricted to generic-level relationships. Here we present the results of a new phylogenetic study of a dataset composed of 9 loci for 26 species of boxfishes using both likelihood and Bayesian methods. Our topology strongly supports the monophyly of both groups, and additionally provides strongly supported resolution for the vast majority of species-level interrelationships. Based on this new phylogeny, we suggest changing the taxonomic status of the species Lactoria fornasini to Tetrasomus fornasini, and Rhynchostracion nasus to Ostracion nasus. Using a Bayesian approach to divergence time estimation we inferred a Paleocene origin of the Ostracioidea, with an estimated origin of the reef-associated ostraciids spanning the Eocene and Oligocene, and a Miocene/Pliocene origin of the aracanids. Copyright © 2012 Elsevier Inc. All rights reserved.