A phylogeny based on nrITS1 and trnL–F sequences resolves the Lejeunea tumida species group polyphyletic with individuals belonging in two clades either side of the basal-most node within Lejeunea. It is impossible for the Lejeunea tumida species group to be more polyphyletic and still be attributed to the same genus under the existing generic classification. A simulation-based approach to testing the null hypothesis of group monophyly rejects this at the P < 0.01 level of significance. Bayesian tests find very strong support for polyphyly, given the data. The monophyly of L. tumida s.s. + L. colensoana is fully supported; however, although Lejeunea tumida s.s. is nested within L. colensoana, this position is not supported. Both L. oracola and L. rhigophila are resolved as monophyletic. Whereas there is moderate support for the monophyly of L. rhigophila, there is no support for the monophyly of L. oracola. Neither is the monophyly of L. oracola + L. rhigophila supported in Bayesian or parsimony analysis.