The Sematophyllaceae s.l. (Sematophyllaceae s.str. + Pylaisiadelphaceae) is one of the most diversified families of pleurocarpous mosses, distributed worldwide. The familial definition and subfamilial delimitation of the family have been controversial since their inception. Phylogenetic analyses were carried out using Bayesian inference, maximum likelihood, and maximum parsimony analyses. Our molecular phylogenetic analysis using five molecular markers (nad5, rbcL, rps4, trnL‐F, and 26S) from mitochondrial, chloroplast, and nuclear genomes revealed the paraphyly of the Pylaisiadelphaceae and the monophyly of Sematophyllaceae s.l. Based on the molecular and morphological evidence, the Sematophyllaceae s.l. were further divided into six subfamilies, Taxithelioideae, Isopterygoideae, Pylaisiadelphoideae, Aptychelloideae, Platygyrioideae, and Sematophylloideae. The Taxithelioideae is established to accommodate Taxithelium, Taxitheliella, and Vernieri, the Isopterygoideae is established to accommodate Isopterygium and Yakushimabryum, the Pylaisiadelphoideae is newly circumscribed to accommodate Brotherella, Pylaisiadelpha, and Orientobryum, the Aptychelloideae is established to accommodate Aptychella, the Platygyrioideae is temporarily established to accommodate Clastobryella, Clastobryum, Gammiella, Platygyrium, and Trachyphyllum, the Sematophylloideae is resurrected to accommodate the Sematophyllaceae s.str., and Isocladiella, Isocladiellopsis, Mastopoma, Heterophyllium, Pseudotrismegistia, Trismegistia, and Wijkia are transferred to the subfamily. A new classification for the Sematophyllaceae s.l. is then proposed.