Cheilolejeuneinae is an early diverging lineage of Lejeuneaceae tribe Lejeuneeae with a pantropical distribution. The current phylogeny and classification of this subtribe is based on morphological and limited-sampling molecular studies. Here we present a molecular phylogeny of Cheilolejeuneinae and related lineages based on maximum parsimony and maximum likelihood analyses, as well as Bayesian inference of two chloroplast regions (trnL-F, trnG) and the nuclear ribosomal ITS1-5.8S-ITS2 region, to test the monophyly of this subtribe, and to re-evaluate the infrageneric classification of Cheilolejeunea. The results confirm the monophyly of Cheilolejeuneinae, which consists of one single genus, Cheilolejeunea. Aureolejeunea and Omphalanthus are nested in Cheilolejeunea and, consequently, all species (11) and varieties (2) accepted in these two genera are transferred to Cheilolejeunea. Based on morphological and molecular evidence a new infrageneric classification of Cheilolejeunea into nine sections is proposed: sect. Anomalolejeunea, sect. Cheilolejeunea, sect. Cyrtolejeunea, sect. Euosmolejeunea, sect. Leucolejeunea, sect. Paroicae, sect. Omphalanthus, sect. Strepsilejeunea and sect. Xenolejeunea. Cheilolejeunea decurviloba is resolved in a sister relationship to Pycnolejeunea densistipula and C. gaoi constitues a separate lineage remote from Cheilolejeuneinae.