Osmanthus fragrans, a well known ornamental plant, is also one of the rareandrodioecious species.Determining the genetic diversity of this species would assist in its conservation and genetic improvement.Data of 10 ancient O.fragrans tree populations were used to assess its genetic diversity and population structure with microsatellite markers.A high level of genetic diversity was observed with POPGENE.The observed and expected heterozygosityof ancient hermaphrodite trees were higher than males, although the number of hermaphrodites was far less than males.Abundant gene exchange between males and hermaphrodites was detected, and trees from the same population often clustered together.Androdioecy is an important factor that determines the genetic structure of O.fragrans and it's urgent to conserve ancient O.fragrans germplasms especially the hermaphrodites.