We describe two new species amongst the most common sponges living on the seabed (inter-reef) of the Great Barrier Reef (GBR) collected during a multi-agency survey (GBR Seabed Biodiversity Project 2003–2006) of the shelf benthic biota using a trawl and dredge at 1254 sites. More than 1,200 sponge morphospecies (operational taxonomic units or OTUs) were recognised, many of which are potentially new species. This paper describes five of the most common sponges, two of which are new to science, Dercitus xanthus sp. nov. and Paracornulum fistulosum sp. nov. Taxonomic revisions of the three other most common species (Coscinoderma nardorus (Lendenfeld, 1886), Spheciospongia vagabunda (Ridley, 1884) and Xenospongia patelliformis Gray, 1858), reveal new characters not previously recorded. Extensive distribution maps are provided for these species within the GBR Marine Park. Analysis of the physical data associated with the biota revealed these species had strong preference for sand and carbonate sediments. As colonisers of the soft seabed these most prevalent species provide important habitat stabilisation, enabling succession communities to more readily establish on the seabed. This wide-scale study along the length and breadth of the GBR provides a concise and encompassing view of the distribution and diversity of the seabed benthos, and has significant implications for the conservation and management of the GBR World Heritage Area.