Alsophila gigantean is a large frond tree fern in family Cyatheaceae. The plant is a vulnerable species that prefers specific subtropical montane climate. Little work has been done so far to access the population genetic variation in A. gigantean. In this study

we developed 15 SSR markers using FIASCO protocol and evaluated these markers in four natural populations from Hainan Island

China. Seven loci proved to be polymorphic. The actual number of alleles ranged from one to nine

and the observed and expected heterozygosity varied from 0 to 0.769

and from 0 to 0.805

respectively. Loci AG-12 and AG-23 were found to significantly deviate from the Hardy-Weinberg equilibrium in populations HNjfl and HNbwl

respectively. Four null alleles were identified. Linkage disequilibrium was further detected at three pairs of loci. Moreover

four SSR markers were verified to be successfully transferred in Alsophila spinulosa.The novel polymorphic SSR markers characterized here will be used to survey population genetic variation and local adaptation in A. gigantean

which helps design effective conservation strategies.