A new species of Brachythecium Schimp., B. canobernabei J.D.Orgaz & J.Guerra is described for Japan based on morphological and molecular data. The species is distinguished morphologically by elongate, acuminate and decurrent ovate-triangular leaves with denticulate margins, subquadrate alar cells becoming rectangular and somewhat inflated in decurrencies, autoicous sexual condition and rough setae. Drawings and light microscope photographs of the new species are provided. A table with the diagnostic characters to distinguish this species from its closest species, and a phylogenetic analysis are also provided.