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Phascolosoma is one of the most important genera of Sipuncula, many species of which including P. similis are economic important species in the fishery of southeast China. However, the current taxonomy determination of P. similis had not been verified yet. Here, we report the complete mitochondrial genome sequence of P. similis. The mitogenome has 16,237 base pairs and made up of a total of 38 genes (13 protein-coding, 23 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. The complete mitogenomes of P. similis will provide useful genetic information for future phylogenetic and taxonomic classification of Phascolosoma.