Three forms of Japanese Eudigraphis (Penicillata, Polyxenidae), which have long been treated as subspecies of Eudigraphis takakuwai (Miyosi, 1947), i.e., E. t. takakuwai (Miyosi, 1947), E. t. nigricans (Miyosi, 1947), and E. t. kinutensis (Haga, 1950), are raised here to three distinct species. Overlap of their distributional ranges over wide areas of Japan was confirmed, and molecular phylogeny using both nuclear (ITS2) and mitochondrial (COI) DNA testified monophyly of each of the three forms. Additionally, the three forms can be easily distinguished from one another by body size, coloration, and habitat, though species identification for the specimens preserved in ethanol is often difficult due to their morphological similarity other than coloration and size. Description of some so-far neglected morphological characters were provided with some SEM photos to supplement knowledge on taxonomy and morphology of the family.