ISSR markers were used to analyze the genetic diversity and genetic structure of 6 natural populations of Camellia pubipetala.Eleven primers were used to amplify DNA samples from 150 individuals,and a total of 92 loci were detected.The genetic diversity of C.pubipetala is relatively high both at the species level and population level.At the species level,the percentage of polymorphic bands (PPB) is 80.43%,Nei’s gene diversity (h) is 0.245 1,Shannon information index (I) is 0.377 6.At the population level,PPB range from 58.70%~66.30%,h range from 0.199 7~0.229 3,I range from 0.300 9~0.343 8.A low level of genetic differentiation among populations was detected based on Nei’s genetic diversity analysis (G_st=0.126 6) and analysis of molecular variance (Φ_st=11.37%).Gene flow (N_m) among the populations is high (3.448 0).A mantel test showed there was a significantly correlation between genetic and geographic distance among the populations studied (r=0.755 1,P<0.05).Relatively high genetic diversity within the population and the low population differentiation of C.pubipetala might be related to its out-crossing mating system and bird pollination.