Phylogenetic relationships and character evolution in the core Ptychanthoideae (Lejeuneaceae, Marchantiophyta), with a focus on Thysananthus, are assessed based on molecular (plastid psbA–trnH, trnG, trnL–F, trnS–rps4, nrITS), morphological–anatomical, and phytochemical data. Generic relationships are molecularly well–resolved and confirm the placement of Mastigolejeunea pancheri and the monotypic Dendrolejeunea fruticosa in Thysananthus. Most morphological characters currently used to distinguish genera in Ptychanthoideae are homoplastic according to ancestral state reconstruction. Molecular and phytochemical data suggest the occurrence of polyphyletic species in Thysananthus and Mastigolejeunea. Careful study of the polyphyletic taxa revealed morphological differences between some of the intraspecific clades, which correlated with synonymized or novel species. Incongruence between plastid and ITS data in M. pancheri indicated the occurrence of a putative hybrid, the first one recorded in Lejeuneaceae and the first in liverworts inferred from phylogenetic data.