Genetic and tribal relationships within the hepatic family Lejeuneaceae are problematic. We studied the phylogeny of the family using sequence data from three genomic regions: 1) the internal transcribed spacer 2 sequence between the nuclear genes encoding 26S and 5.8S ribosomal RNA, 2) partial sequences of the chloroplast genes trnL and trnF including the spacer between them, and 3) the partial sequence of the chloroplast gene, rbcL. Seventeen species representing the subfamilies Ptychanthoideae and Lejeuneoideae as well as the tribes Nipponolejeuneae, Lejeuneae, and Cololejeuneae were included. The family as a whole seems to be monophyletic, with the exception of the genus Nipponolejeunea that is closer to the genus Jubula. Our results also support the existence of two main subfamilies, Lejeuneoideae and Ptychanthoideae. The representatives of the genus Cololejeunea are basal in the Lejeuneoideae clade in our tree, supporting tribal, rather than subfamilial position for the Cololejeuneae. The relationships of the Lejeuneaceae, Jubuloideae, and Frullania remain unresolved in our analyses.