A new species Polacanthoderes shiraseae sp. nov. from three Antarctic regions (off Cape Darnley, off Totten Glacier, and in Lützow-Holm Bay) is described. In addition, type species of Polacanthoderes, Polacanthoderes martinezi, is redescribed. The new species is distinguished from P. martinezi by the presence of conspicuously thick lateroventral acicular spines on segments 8 and 9 and the presence of sublateral small acicular spines on segment 7. Both P. martinezi and P. shiraseae sp. nov. occasionally show intraspecific morphological variations in the position of some small acicular spines. The K2P genetic distances based on the mitochondrial cytochrome c oxidase subunit 1 gene sequences in P. shiraseae sp. nov. are 0–1.5%, equivalent to those in other echinoderid species. Phylogenetic analyses of Polacanthoderes based on the nuclear 18S rRNA and 28S rRNA gene sequences support the inclusion of the genus in Echinorhagata/Echinoderidae and suggest that the genus represents the most basal group of this order/family.