Haplomitrium minutum (E.O.Campb.) J.J.Engel & R.M.Schust., considered to be a little-known species endemic to New Zealand, had been reported to grow on Mt. Ainodake, central Japan. However, after revision of the herbarium material corresponding to the previous record and examination of additional material, including male plants, we concluded that original determination is erroneous. Instead, these plants are merely an environmental modification of Haplomitrium hookeri (Lyell ex Sm.) Nees, widely distributed in the Northern Hemisphere. On the basis of morphological and molecular phylogenetic analyses using chloroplast DNA (rbcL and trnL–F), we excluded H. minutum from the Japanese flora. Taxonomic identity of the plants from Mt. Ainodake, morphological variation in H. hookeri depending on habitat differences, and morphological differences between H. hookeri and H. minutum are discussed. We also provide new information on morphological variations of elaters and antheridial stalks in H. minutum based on the type specimen.