Heteroscleromorpha with approximately 5000 species is the largest and most important group of Demospongiae in terms of number of species. The aim of this project was to reconstruct a robust phylogeny of Heteroscleromorpha using 28S rRNA and mitochondrial COI barcoding fragments. The phylogenies derived from the 28S and COI sequences were congruent but conflicted with the morphological classification of Systema Porifera (Hooper & van Soest, 2002). Fourteen well supported clades were recovered and formed the basis for a new hypothesis for relationships of taxa allocated to Heteroscleromorpha. At the time of publication this was the largest and most comprehensive study of Heteroscleromorpha. Several important taxonomic changes were proposed including the resurrection ofAxinellida for a clade containing Axinellidae, Raspailiidae and Stelligeridae. The decision to abandon Axinellida arid distribute its families among other orders was based on the more parsimonious assumption that an axially condensed skeleton had evolved independently in separate lineages in preference to the less parsimonious assumption that asters, acanthostyles and sigmata each evolved more than once. In an attempt to understand the underlying causes of the incongruence between the morphology based classification Systema Porifera and the molecular classification, the distribution of asters, acanthostyles, sigmata and axially condensed skeletons were mapped onto phylogenetic trees derived from combined full length 18S rRNA, partial 28S rRNA (03-08 region) and COI barcoding sequences. From their distribution on the tree it was demonstrated that asters, acanthostyles, sigmata and axially condensed architectures are all homoplasious characters. The family Stelligeridae was resurrected for a strongly supported clade containing Halicnemia spp. (currently classified as Heteroxyidae), Stelligera spp. and Paratimea spp. (both genera classified as Hemiasterellidae). The surprising discovery that taxa from such distant parts of the classification appeared to be closely related on the 28S, 18S and COI trees led to a more extensive investigation of Heteroxyidae and Hemiasterellidae. Several species assigned to Heteroxyidae (on the basis of the possession of smooth or acanthose microxea) and Hemiasterellidae (on the basis of the possession of smooth or partially microspined euasters) were shown to be more closely related to other heteroscleromorph families.