We describe and illustrate two Strobilomyces species, S. seminudus and S. hongoi sp. nov. These two species have been confused and treated as a single species (i.e. S. seminudus). However recent studies based on population genetics have implied that they are reproductively isolated. In the present study we found that they are phylogenetically and morphologically distinct. The molecular phylogenetic trees inferred from the partial sequences of the largest subunit of RNA polymerase II (RPB1) and the second-largest subunit of RNA polymerase II (RPB2) support the differentiation of these two species as well as their differentiation from other related species. Strobilomyces seminudus is characterized by a stipe with an annular zone, becoming distinctly thickened near the apex and mottled with appressed-tomentose scales near the base. In contrast S. hongoi is characterized by a stipe with a remarkable reticulum at the upper and middle part and with minutely warty scales downward. Stipe characteristics also are useful for distinguishing these two species from other related species. In addition the incompletely reticulated basidiospores of these two species are also distinct from those of related species (i.e. S. foveatus).