We explored molecular data in order to establish the phylogenetic relationships of the Thuidiaceae. We sampled nine genera and 13 species of Thuidiaceae, and included representatives of 15 families that have been considered related to Thuidiaceae at some point. We used two chloroplast codifier genes (rbcL and rps4) and the rps4-trnS intergenic spacer. Our combined parsimony analyses retrieved a clade containing 12 exemplars of Thuidiaceae representing eight genera (Thuidium, Thuidiopsis, Pelekium, Aequatoriella, Abietinella, Rauiella, Haplocladium and Actinothuidium) but with the inclusion of Leskea polycarpa and exclusion of Hylocomiopsis making the Thuidiaceae non-monophyletic as currently defined, and the Leskeaceae polyphyletic. The name Thuidiaceae is retained for the informal “thuidioid” group of taxa. The Rhytidiaceae (Rhytidium rugosum) was found sister to the clade of Thuidiaceae s.lat and Leskea polycarpa. The rps4-trnS spacer added characters that improved resolution and may be of value for similar studies at family level in other pleurocarpous mosses.