For reveal differences and characteristics of Pinus latteri Mason natural populations in Bawangling forestry area of Hainan province on the level of genetic diversity, SSR molecular markers technique were used to study genetic diversity of 350 single individual plants representing 6 nature populations of Pinus latteri Mason. The result showed that 38 alleles were detected using 12 polymorphic SSR primers. The observed heterozygosity (Ho), expected heterozygosity (He), Shannon information index (I) and Nei′s expected heterozygosity were 0.1933-0.4679, 0.4150-0.5321, 0.5225-0.7384 and 0.3451-0.4819, respectively. Pinus latteri Mason had a low genetic diversity level among populations in Bawangling. The proportion of genetic differentiation among the populations accounted for 0.0628, Most of variation (97.8%) appeared inner population and there were not gene differentiations among populations. The 6 populations were divided into 2 groups based on genetic distance，showing that the genetic distance was less significantly affected with the geographic latitude，but was not strictly according to the geographic distance clustering, which was influenced by natural geographic isolation.