Abstract: Individuals of Macromitrium cavaleriei Card.& Thér.vary in morphological traits.To know whether such morphological variation of the species has a genetic background,we applied random polymorphic DNA(RAPD)markers to detect genetic diversity using four different Macromitrium cavaleriei populations collected from Fengyangshan(Southern Zhejiang),Jinhua Beishan(Middle Zhejiang),Xitianmushan(Northwestern Zhejiang)and Lushan of Jiangxi.We screened 15 effective primers from 100 random primers,and found 183 amplification sites,which included 145 polymorphic sites,accounting for 79.69% polymorphic loci.We found that:(1)genetic distances among the four populations varied from 0.0732 to 0.1514,Nei’s gene diversity(H)was 0.3378,Shannon’s diversity index(I)was 0.5126,and genetic differentiation coefficient(G_st)was 0.2521,and gene flow among populations(N_m)was 2.4947;and(2) the genetic diversity within populations was 0.4055 on average,accounting for 79.11% of the total genetic diversity of the four populations.The above results showed that Macromitrium cavaleriei had lower genetic diversity,more genetic variations existed within populations than among populations,and the morphological variation of M.cavaleriei had little genetic background,which is mainly caused by ecological factors.Cluster analysis showed that there was no direct correlation between genetic distance and geographic distance.The genetic diversity was related to species traits and habitats.Although rich morphological variations existed within populations,they belonged to the same species.