Lithophyllum okamurae is one of the important encrusting coralline algae, which plays important roles as primary producer, carbonate sediment builder, and habitat provider in the marine ecosystems. In this study, L. okamurae was collected from tropical coast of Sanya, and firstly described based on both detailed morph-anatomical characteristics and molecular studies of typic DNA sequences. The structure of the thalli of L. okamurae was pseudoparenchymatous construction with radially organized dimerous organizations in the crustose portion. The pseudoparenchymatous construction were composed of three parts, including 1 to 3 layers of epithelia cells which had flatten to round outermost walls, one layer of square or rectangular cells of the hypothallia and multiple layers of square or elongated rectangular peripheral cells. Palisade cells were observed, and the cells of the contiguous vegetative filaments were connected by secondary pit-connections with cell fusions absent. The carposporangial conceptacles, the spermatangial conceptacles, the bisporangial conceptacles and the tetrasporangial conceptacles were observed, and all these four kinds of conceptacles were uniporate. The spermatangial conceptacles were slightly convex and buried at shallow depths in the thalli tissues, and the carposporangial conceptacles and asexual conceptacles were protruding and conical. Phylogenetic studies based on DNA barcoding markers of 18S rDNA, COI, rbcL and psbA revealed that L. okamurae clustered with the closest relation of L. atlanticum, and formed a distinct branch. Based on the comparative anatomical features and the molecular data, the detailed description of the valid species of L. okamurae was firstly given in this study to provide theoretical basis for algae resources utilization and conservation in marine ecosystems.