To clarify the phylogenetic relationships of Pseudobiantes japonicus Hirst, 1911 and its allied species, Epedanellus tuberculatus Roewer, 1911 and Kilungius insulanus (Hirst, 1911) (Arachnida: Opiliones: Laniatores: Epedanidae), we conducted morphological and nucleotide sequence analyses of this complex. Sequencing of the cytochrome c oxidase subunit I gene of 179 samples recovered six clades comprised of four allopatric lineages within P. japonicus and two monophyletic groups of E. tuberculatus and K. insulanus, respectively, related as follows: ([Clades A B of P. japonicus] [Clade C of P. japonicus]) (K. insulanus [Clade D of P. japonicus E. tuberculatus]). This phylogenetic relationship implies that “Pseudobiantes japonicus” is paraphyletic or polyphyletic, unless mitochondrial introgression between species is postulated. Moreover, Clades C and D of P. japonicus were also separable by the combination of a few morphological characters and from Clades A and B in P. japonicus. These results suggest that a thorough taxonomic revision is needed for the classification of P. japonicus and allied species.