Racoleus japonicus is described as a new species. It is characterized by a blackish brown minutely filamentous thallus with lateral spines, vertical arrangement of hyphae with uneven and undulate to corrugated hyphal walls, and a Trentepohlia photobiont. In this genus, only R. trichophorus was known before the present study. Racoleus japonicus is distinguished from that species by having broader filaments (10–15 μm wide), larger hyphal cells (10–20 × 3–7 μm), and lateral sinuous spines. It was collected on shady rocks from northern to southern Japan at elevations between 290 and 1700 m. A molecular phylogeny based on nuSSU, nuLSU and mtSSU inferred that R. japonicus has a close relationship with unidentified fungi of Capnodiales, and that is not related to Cystocoleus and Racodium which have similar filamentous thalli. Based on the molecular phylogenetic analyses, R. japonicus is classified within Teratosphaeriaceae.