We establish a new genus of planocerid polyclad, Heteroplanocera gen. nov., based on a new species, H. katoi sp. nov., collected at a depth of 245 m off the coast of the Izu Peninsula, West Pacific, Japan. Heteroplanocera gen. nov. is distinguished from other planocerid genera by the following characteristics: (i) a pair of nuchal tentacles, (ii) a muscular bulb, (iii) a pair of spermiducal bulbs (instead of a seminal vesicle), (iv) a free prostatic vesicle, (v) a pair of accessory organs with teeth, (vi) a Lang's vesicle, and (vii) the lack of a bursa copulatrix. We provide a partial sequence of the cytochrome c oxidase subunit I (COI) gene (712 bp) as a DNA barcode of the new species. Furthermore, we estimate the phylogenetic position of Heteroplanocera gen. nov. among Planoceridae based on partial sequences of COI and 16S, 18S, and 28S ribosomal DNA. Based on our findings, we discuss the evolution and function of the (i) vaginal cuticularized structure and (ii) accessory organs among planocerid flatworms.