Twenty-two polymorphic primer pairs were selected from 53 SSR special primer pairs developed and designed by our laboratory to amplify genomic DNA of 46 litchi. 23 locus-specific SSR markers were obtained, and 52 alleles were found and the average alleles per marker was 2.4. The average observed heterozygosity, expected heterozygosity and PIC of all markers were 0.451, 0.355 and 0.507 respectively. Locus Lit6 had the highest number showed that it was an optimal marker. Then the selected polymorphic SSR markers were used to detect the genetic diversity of 46 litchi germplasm and to cluster them. The results revealed that similarity coefficients of most of litchi germplasm were among 0.63-0.95, which indicated that the genetic relationships between them were closer related. In addition, it was identified that huaizhi(hainan) and huaizhi(guangdong) were not the same cultivar but the different one which used the same name.