The integration of morphological and molecular markers is essential in the recognition of inter- and intraspecific variability, as well as to distinguish species. Spicular characters of the excavating sponge Cliona mucronata Sollas, 1878 were reported to vary depending on sample origin, suggesting the existence of an unrecognized species complex. We analyse specimens from central Indo-Pacific, Eastern Tropical Pacific (ETP) and the south-western Caribbean in a morpho-molecular approach. All specimens were in alpha morphology and had two types of tylostyles, a slimmer-longer and a wider-shorter one. Spicule measurements from 35 specimens resulted in three morphologically distinct clades consistent with the perceived species and the region of provenance. Molecular markers COI mtDNA and 28S rDNA of the Mesoamerican material showed a well-supported separation between these species and confirmed our morphological results. Based on the above evidence we described two new species, Cliona mariae sp. nov. from the ETP and Cliona yorkin sp. nov. from the south-western Caribbean Sea. Both are close to, but different from C. mucronatasensu stricto. We also detected intraspecific variability within C. mariae sp. nov. along the ETP. A circumtropical distribution of C. mucronata is here rejected, and we propose that other species of excavating sponges with a wide distribution in different oceans need to be carefully reviewed as well. http://zoobank.org/urn:lsid:zoobank.org:act:453CFFBC-9F22-471C-9AC5-42E970133A75 http://zoobank.org/urn:lsid:zoobank.org:act:CE75AB79-2569-48AE-AA70-B6B9CA2FE340.