Recent molecular studies have shown that the sponge order Haploslcerida is polyphyletic as the freshwater sponges appear to be more closely related to other demosponges than they are to the marine haplosclerids. Within the marine haplosclerid clade relationships viewed via 18S and 28S rRNA gene phylogenies suggest that the suborders and many families and genera are also polyphyletic. However, both of these genes are on the same locus and do not evolve completely independently. We have analysed mitochondrial Cytochrome oxidase 1 gene fragments from 44 species of marine Haplosclerida and show conclusively that the classification of this group needs complete revision. Molecular data show a very complicated phylogeny supporting very few morphological hypotheses and little geographical pattern. However, the molecular data contain a great deal of phylogenetic signal at many taxonomic levels and support phylogenies drawn from the other genes.