Huperzia serrata,an important traditional Chinese herb,has become a threatened species resulting from over-exploitation and habitat fragmentation in China.We assessed the levels and pattern of the genetic variation within and among four populations of this species in Wuling Mountains area using amplified fragment length polymorphism (AFLP) markers.(1)Seven primer combinations used in the study amplified 615 discernible bands with 549 being polymorphic,indicating a considerable high level of specific genetic diversity (at species level:percentage of polymorphic loci PPB=89.27%,effective number of alleles N_e=1.257,Nei’s gene diversity H=0.178,and Shannon’s information index I_sp=0.298;at population level:PPB=71.42%,N_e=1.235,H=0.154,and Shannon’s information index I_pop=0.251).The differences among populations in levels of genetic diversity were obvious,with the highest level (PPB=81.95%) in PBY population and the lowest level (PPB=64.55%) in TFS population.(2)A low level of genetic differentiation among populations was detected based on Nei’s genetic diversity analysis (G_ST=0.159),Shannon’s diversity index (0.16).Further AMOVA analysis also revealed a low level of genetic differentiation among populations (Φ_ST=0.242,P＜0.001).(3)An extraordinarily high level of gene flow (N_m=2.647) may result from out-breeding and extensive wind-dispersal spores.(4)Nei’s genetic identity (I_N) values between population pairs ranged from 0.927 9～0.969 4.A Mantel test showed no significant correlation between genetic distance and geographical distance (r=0.269,P=0.887),suggesting that the gene flow be not restricted geographically.In general,population genetic diversity and genetic structure are mainly determined by population history.The level of the genetic diversity in the less disturbed and stable populations which are dominated by clonal reproduction is lower than those of new young populations which are built by sexual reproduction.A number of factors that might affect the genetic profiles of H.serrata include clonal growth,selective effect of niche and outcrossing,as well as the effective wind-dispersal of spores.