A new species of the polyclad genus Prosthiostomum is described from the intertidal zone of the South China Sea, Huidong, China, based on morphological and molecular analyses. Prosthiostomum huidongense sp. nov. is characterized by i) few marginal eyes scattered between the marginal band and the cerebral eyes; ii) sucker located at two-thirds of the body length, being removed from the female gonopore by twice the distance between the male and female gonopores; iii) shallow male atrium with slightly ruffled inner wall, positioned approximately perpendicular to the body wall. Molecular phylogenetic analyses based on 28S rDNA sequence showed that the new species was nested in a clade composed of Prosthiostomum species. The uncorrected p-distance of COI between P. huidongense sp. nov. and other Prosthiostomum species ranged from 20.3 to 24.3%, and the high genetic divergence further supports P. huidongense as a new species.