Abstract: Phylogenetic relationships within Huperziaceae were studied using chloroplast rbcL gene and psbA-trnH intergenic spacer sequences. In the rbcL sequence analysis, 25 species were analyzed and they were resolved into two major clades. One clade corresponded with sections Huperzia and Serratae of the genus Huperzia, while the other clade contained Phlegmariurus and the tropical species of Huperzia. Therefore, Phlegmariurus is derived from Huperzia. In the psbA-trnH sequence analysis, 17 species were sampled and they were resolved into two major clades with high bootstrap values. Both Chinese species of Huperzia and Phlegmariurus formed sister groups, and within Chinese Huperzia, sect. Huperzia and sect. Serratae formed sister groups.