We herein describe a new species of stylochoplanid flatworm, Alloioplana yerii, from Japan. This is the first record of the genus from the West Pacific. Alloioplana yerii is characterized by i) a lack of nuchal tentacles, ii) an oval prostatic vesicle that is smaller than the seminal vesicle, iii) the presence of a common sperm duct, and iv) the presence of an intra-prostatic ejaculatory duct. 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 18S and 28S ribosomal DNA and of COI suggest that Stylochoplanidae is not monophyletic and that Al. yerii forms a relatively well-supported clade with Echinoplana celerrima (Gnesiocerotidae) and Notoplana sp. (Notoplanidae).