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Phascolosoma perlucens is one of the most common intertidal sipunculan species and has been considered a circumtropical cosmopolitan taxon due to the presence of a long-lived larva. To verify whether P. perlucens is a true cosmopolitan species or a complex of cryptic forms, we examined the population structure and demographics of 56 putative P. perlucens individuals from 13 localities throughout the tropics. Analysis of two mitochondrial markers, cytochrome c oxidase subunit I and 16S rRNA, suggests high levels of genetic differentiation between distantly located populations of P. perlucens. At least four different lineages identified morphologically as P. perlucens were distinguished. These lineages are likewise supported by phylogenetic analysis of the two mitochondrial markers and by the haplotype network analysis. Our results suggest that P. perlucens is a case of overconservative taxonomy, rejecting the alleged cosmopolitanism of P. perlucens. However, cryptic speciation also exists in some areas, including a possible case of geminate species across the Isthmus of Panama.