An unidentified Siler species has been recorded from the central Ryukyus in Japan, but the taxonomic status of the species has not been clarified sufficiently until now. To make clear the taxonomic identity of the species, in addition to a morphological comparison with other Japanese congeners, we performed molecular analysis based on partial sequences of mitochondrial cytochrome oxidase subunit I (mt-COI). As the results, we concluded the unidentified species from the central Ryukyus is new to science. Therefore, we describe this species as Siler rubrum sp. nov. in the present paper. Siler rubrum sp. nov. is very similar to S. collingwoodi (O. Pickard-Cambridge, 1871). However, males of S. rubrum sp. nov. can be distinguished from the latter by the length of the tibial apophysis and the shape of the tegulum on the pedipalp. Females of S. rubrum sp. nov., in contrast, lack distinct diagnostic characters compared with males, but can be distinguished from S. collingwoodi by slight differences in the shape of the copulatory duct.