Cystoathyrium chinense Ching, the sole representative of Cystoathyrium, is a critically endangered species endemic to China with no more than 40 extant individuals. Until now, its systematic position and relationships among leptosporangiate ferns remained unknown. The present study assessed the phylogenetic relationships of Cystoathyrium chinense with potential relatives densely sampled using three chloroplast DNA markers (matK, rbcL, and trnG-R intergenic spacer). Our results support the inclusion of Cystoathyrium in Cystopteris. A hybrid origin hypothesis of Cystoathyrium chinense is neither supported nor rejected by the present study. According to our ancestral area reconstruction analysis, the disjunct distribution of Cystoathyrium and its closely related North American taxa may be attributed to the long-distance dispersal by way of Beringia. Consequently, a new combination (Cystopteris chinensis comb. nov.) is made, and the description is supplemented based on our new observations in the field.