Abstract: Pteridophytes are the second-largest group of vascular plants,and understanding its genetic diversity could provide scientific basis for both conservation and utilization.In this paper,we briefly introduced the reproductive mode of pteridophytes and summarized the application of molecular methods in the researches of genetic diversity emphatically.It included three aspects: species relative and classification,genetic diversity and genetic structure,and molecular phylogeography.Finally,The problems in the current researches were discussed and nearfuture perspectives on the subject were put forward.