Sponges belonging to the class Homoscleromorpha have become a pivotal group to help understand early metazoan evolution. However, their complex systematics and cryptic habitat (e.g. dead coral, or under/amongst coral rubble or rock), hinders the recognition and classification of species. An extensive study carried out in coral reefs from the Mexican Pacific coast, Revillagigedo and Clipperton Islands, yielded 21 specimens and five species of Plakinidae: Plakortis albicans, Plakinastrella clippertonensis, Plakina muricyae sp. nov., Plakina paradilopha sp. nov., and Plakortis clarionensis sp. nov. Fragments of cytochrome c oxidase subunit I (cox1) and cytochrome b (cob) mtDNA were sequenced to generate DNA-barcoding of some species and to determine their phylogenetic relationships with other homosclermorphs. Molecular and morphological data placed Plakina muricyae sp. nov. together with the morphologically related species Plakina monolopha (Plakina monolopha-complex), whereas Plakina paradilopha sp. nov. seems to belong to the Plakina dilopha complex. According to spicule morphology and size, Plakortis albicans had been considered to be in the Plakortis simplex-complex. However, this was not supported by our molecular data and Plakortis albicans clustered with Plakinastrella sp. here. This is the first time that the standard cox1 ‘barcoding fragment’ has been analysed for the systematics of Plakinidae, which showed to Plakina as a monophyletic group, which is congruent with the morphological hypothesis. The genus Plakina is here recorded for first time from Mexican Pacific waters. A taxonomic key for Homoscleromorpha species from the eastern Pacific region is also included. © 2014 The Linnean Society of London