Cryptothecia and Myriostigma are important elements of crustose lichen communities in tropical to subtropical forests, but little research has been done on these two genera in China. Morphological and molecular phylogenetic approaches to investigate species diversity of Cryptothecia and Myriostigma from Southern China were carried out in this study. We find five species of Cryptothecia and Myriostigma in our study, including three new species (M. flavescens, M. hainana and M. laxipunctata) and two new records (C. bartlettii and C. inexspectata). In addition, a phylogenetic tree based on mtSSU, RPB2 and nLSU illustrates the placement of the five species and supports the delimitation of the three new taxa. Detailed descriptions of morphological, ecological and chemical characteristics and illustrations are provided for every species. A key to all known Chinese Cryptothecia and Myriostigma species is also provided.