Abstract: Analysis on the genetic diversity of 11 natural populations of Betula luminifera was carried out in Fujian Province.Thirty-four reliable primers(25 RAPD primers, nine ISSR primers) were chosen to amplify DNA samples from 77 individuals of 11 natural populations of B. luminifera. Based on the 25 RAPD primers, a total of 270 bands were generated, among which polymorphic bands accounted for 98.52% and the number is 267. Based on the nine ISSR primers, 113 bands were produced and all of them were polymorphic bands. The results of research showed that among the 11 natural populations, those in Luobuyan Nature Reserve of Shaxian County and Liangye Mountain Nature Reserve of Wuping County had the highest genetic and gene diversity and richness, while the population of Sanyuan County had the least one. Also the genetic and gene diversity within populations was obviously higher than that among the populations. It also showed that the similarity index between Weimin County and Luobuyan Nature Reserve of Shaxian County was the least.Based on RAPD and ISSR markers, the 11 natural populations were divided into two clusters according to the UPGMA cluster analysis, although the differences between RAPD and ISSR markers were observed. All of the results lay a foundation for the future genetic improvement of %B. luminifera%.