We describe a new species of ilyplanid polyclad, Zygantroides serpulidicola sp. nov., from Amakusa, Kumamoto, Japan. This is the third member of Zygantroides Faubel, 1983 and the first record of the genus from the Pacific Ocean. Zygantroides serpulidicola sp. nov. is characterized by i) the mouth opening near the common gonopore, ii) the sperm ducts separately entering a pear-shaped seminal vesicle, iii) an elongated Lang’s-vesicle duct, and iv) the horseshoe-shaped Lang’s vesicle located posterior to the common gonopore. We provide a partial sequence of the mitochondrial cytochrome c oxidase subunit
I (COI) gene (712 bp) as a DNA barcode for the species. Our phylogenetic analyses based on concatenated sequences of the 16S, 18S, and 28S ribosomal DNA and COI indicate that Z. serpulidicola sp. nov. is nested in a clade comprised of Discocelidae and Ilyplanidae; the latter does not appear to be monophyletic.