Two new taxa in the moss genus Fissidens are described from aquatic habitats in New Zealand: F. waiensis sp. nov. and F. rigidulus Hook.f. & Wilson var. pseudostrictus var. nov. Fissidens perangustus Broth., a species known previously only from Australia, is recognised in New Zealand, and a lectotype designated. The presence of F. bryoides Hedw. in New Zealand is confirmed, based on modern collections. Fissidens variolimbatus Allison and F. leptocladus Müll.Hal. ex Rodway var. cheesemanii Dixon are placed in the synonymy of F. leptocladus var. leptocladus; F. australiensis A.Jaeger is reduced to a variety of F. tenellus Hook.f. & Wils.; and the new combination F. tenellus var. leptochaete (Dusén) J.E.Beever & I.G. Stone is made.