Sipunculan taxonomy relies on a limited set of external morphological and internal anatomical characters. In addition, this marine group is characterized by an unusual large number of putatively cosmopolitan species. However, this ‘cosmopolitan’ status could be an artifact of their conserved morphology and the small number of unambiguous taxonomic characters available for delimiting species. Species delimitation can therefore be aided by molecular techniques. We investigated the case of the widespread and common species Sipunculus nudus Linnaeus, 1766 to determine its systematic validity. We analysed the morphology of multiple specimens of S. nudus collected from 11 localities around the world and undertook phylogenetic analyses using molecular sequence data from four genes (28S rRNA, 16S rRNA, histone H3 and cytochrome c oxidase subunit I). High levels of genetic differentiation are present between distantly related populations of the putative species S. nudus. Five distinct lineages were identified by phylogenetic analyses, three of which – the best-represented populations – can be distinguished morphologically. Our phylogenetic and morphological analyses thus do not favor the cosmopolitan status of S. nudus, suggesting instead that it constitutes a complex of morphologically similar but distinguishable species.