Cryptromeria fortunei is one of the main forest plantation species in the subtropical high altitude areas in China. In this paper we collected 49 C. fortunei germplasm resources and provides a study of the utility of freely available C. japonica EST resources for the development of markers necessary for genetic diversity analyses of C.fortunei. By screening 24,299 EST sequences from C.japonica with SSR Finder, we identified 2384 ESTs carrying 2783 SSR motifs. We successfully obtained 364(15 %) primers from 2419 putative SSR loci. Of the 80 candidate SSR markers tested, 70(87.5 %) yielded stable and clear PCR products. With those primers, the genetic diversity of 49 C. fortunei we collected was studied. The results showed that 18 primers yield polymorphism within these accessions. These 18 primers generated 48 scorable SSR loci and the average number of polymorphic SSR loci per primer was 2.7. The PIC value varied from 0.375 to0.8101, with the average of 0.4780. The Shannon index is0.5718, and the value of the observed number of alleles and effective number of alleles are 1.9167 and 1.7289,respectively. The genetic coefficient of these 49 accessions varied from 0.28 to 0.87. According to the genetic distances, a cluster tree was constructed. At genetic coefficient of 0.60, these 49 accessions can group into 3: group Ⅰ contains only FJ-laizhou accession, and group Ⅱ contains 2 accessions from FJ-layang, and the other one group contains mixed accessions. At genetic coefficient of 0.68, the former groupⅡwas constructed into 7 subgroups, with the first 3 subgroups contain 16 accessions in which 11(69 %)are from Fujian province, and the later 4 subgroup contain31 accessions in which 20(65 %) were from Zhejiang province. Cryptromeria fortunei is one of the main forest plantation species in the subtropical high altitude areas in China. In this paper we collected 49 C. fortunei germplasm resources and provides a study of the utility of freely available C. japonica EST resources for the development of markers necessary for genetic diversity analyzes of C. fortunei. By screening 24, 299 EST sequences from C. japonica with SSR Finder, we identified 2384 ESTs carrying 2783 SSR motifs. We successfully obtained 364 (15%) primers from 2419 putative SSR loci. Candidate SSR markers tested, 70 (87.5%) yielded stable and clear PCR products. With those primers, the genetic diversity of 49 C. fortunei we collected was studied. These results showed that 18 primers yield polymorphism within these accessions. These 18 primers generated 48 scorable SSR loci and the average number of polymorphic SSR loci per primer was 2.7. The PIC value varied from 0.375 to0.8101, with the average of 0.4780. The Shannon index is 0.57 18, and the value of the observed number of alleles and effective number of alleles are 1.9167 and 1.7289, respectively. The genetic coefficient of these 49 accessions varied from 0.28 to 0.87. According to the genetic distances, a cluster tree was constructed. At genetic coefficient of 0.60, these 49 accessions can group into 3: group I contains only FJ-laizhou accession, and group II contains 2 accessions from FJ-layang, and the other one group contains mixed accessions. At genetic coefficient of 0.68, the former group IIwas constructed into 7 subgroups, with the first 3 subgroups contain 16 accessions in which 11 (69%) are from Fujian province, and the later 4 subgroup contain 31 accessions in which 20 (65%) were from Zhejiang province.