A molecular phylogeny to test the monophyly of Nephelolejeunea by using previously published nrITS, rbcL and trnL–F sequence data demonstrated that Nephelolejeunea is paraphyletic with respect to Siphonolejeunea. Nephelolejeunea and Siphonolejeunea are, therefore, merged and, as the latter name has priority, new combinations in Siphonolejeunea are made for 10 species. The valid publication of the name Austrolejeunea is re-evaluated and we conclude that both Siphonolejeunea subgenus Austrolejeunea and Siphonolejeunea olgae were validly published in 1963. Siphonolejeunea bidentata is reported as new for New Zealand on the basis of a collection from the Wairarapa, a new species, Siphonolejeunea raharahanehemiae, is described on the basis of recent collections from Te Paki, where it grows on the twigs of Metrosideros bartlettii (Myrtaceae), and we provide a revised key to species of Siphonolejeunea. The significant conflict in signal between nrITS and chloroplast markers associated with the relationships of Cololejeunea angustiflora, which chloroplast sequence data suggest may not be grouped with the rest of Cololejeunea, is another interesting result from the phylogeny. The relationships of Cololejeunea angustiflora and its allies warrant further investigation.