An extinct moss species Muscites kujiensis is described based on a plant fragment preserved in Late Cretaceous (Santonian, 83–87 Ma) amber from the Kuji district, northern Honshu, Japan. It is characterized by (1) small size of the shoot, less than 5 mm wide, (2) distant leaf arrangement, (3) oblong leaves with a single costa, (4) entire leaf margins without bordered cells, and (5) transparent outer layer of stem. The lack of apical parts of the shoot, reproductive structures and sporophytes prevents us from giving a more extensive comparison of M. kujiensis to extant species, but the characters observed in this species suggest an affinity to Bryopsida. Along with the spore genus Stereisporites (Sphagnaceae) and Polytrichites aichiensis, which is based on transverse sections of a fossilized stem, M. kujiensis is one of the few fossil mosses reported from Japan and the first unequivocal evidence of fossilized moss shoots found in Japan, an important addition to our knowledge of Late Cretaceous mosses from East Asia.