Polynesia is a hotspot for marine biodiversity in the South Pacific Ocean, yet the distribution of many invertebrate taxa in this region is still often poorly assessed. Information on the diversity and phylogeography of sponges in particular remains limited in spite of their importance for coral reef ecosystems. Recent expeditions to the island group of Wallis and Futuna enabled the first larger-scale assessment of the Wallis Island sponge fauna, resulting in the molecular identification of 82 unique Molecular Operational Taxonomic Units (MOTUs) from 339 sponge samples based on 28S C-region rDNA and CO1 mtDNA data. Faunal comparisons with both adjacent archipelagos and more distant Indo-Pacific regions were predominantly based on the MOTUs obtained from Wallis Island ecoregions, and suggest high levels of endemism of sponges in Wallis and Futuna, corroborating previous data on the biodiversity of sponges and other marine phyla in the South Pacific. The results of this molecular taxonomic survey of the Wallis and Futuna sponge fauna aim to lay solid foundations for a sustainable ‘Blue Economy’ in Wallis and Futuna for the conservation of their local coral reefs.