Sponges that excavate and inhabit calcareous substrate, predominantly of the Clionaidae, are widely distributed in marine habitats, but are particularly diverse and abundant on coral reefs. Unfortunately, their cryptic habit and difficult taxonomy mean respective taxa are poorly understood, and therefore they are rarely included in reef surveys. This is particularly true of the Southeast Asian Indo-Pacific, where a diverse faunistic record is contrasted with a very limited understanding of eco-physiological requirements of these sponges. In light of this, in situ surveys of the most common bioeroding sponges in the Wakatobi region of Southeast Sulawesi, Indonesia were conducted, followed by morphological and molecular analysis. The seven most common species in the Wakatobi included five species with a wide Indo-Pacific distribution and two new species. Four species, Cliona orientalis, Cliona aff. schmidtii, Spheciospongia cf. vagabunda trincomaliensis and Cliothosa hancocki have been previously reported from Indonesian waters, while Zyzzya criceta is a new record for Indonesia. Two brown sponges belonging to the Cliona viridis species complex, Cliona wakatobiensis sp. nov. and Cliona cribripora sp. nov., are here described as new to science. They were morphologically distinct from other species in the sample region and could not conclusively be allocated to any other known clionaid species. A maximum likelihood analysis of ITS1 rDNA revealed them to be phylogenetically closer to other Indo-Pacific species such as Cliona orientalis and Cliona thomasi than to other species within this taxon complex.