A monographic study of the genus Thelotrema in Japan is made. The morphology, anatomy, chemistry, ecology and distribution of Japanese 16 species are discussed. A key to species identification and distribution maps of the species are presented. Five species are described as new to science: T. boninense Tat.Matsumoto, T. canescens Tat. Matsumoto, T. grossomarginatum Tat.Ma tsumoto, T. infundibularis Tat.Matsumoto and T. nipponicum Tat.Matsumoto. T.fauriei is a synonym of T. similans. The first record from Japan is made for the following five species: T. alborosellum, T. dilatatum, T. imperfectum, T. nureliyum and T. patens. Genus Thelotrema in Japan is divided into two sections by thalline exciple and paraphyses characters: sect. Thelotrema and sect. Asteristion (Leight.) Tat.Matsumoto stat. nov