Disanthus including one species and one variety, is a small eastern Asian genus of the family Hamamelidaceae. D. cercidifolius , which occurs in Japan and D. cercidifolius var. longipes , which only occurs in south China. D. cercidifolius var. longipes was listed in the Red List of Endangered Plant Species and Second Grade of the List of Wild Plants Under State Protection in China. This species is significant for the study of phylogeny and floristic geography in east Asia. However, the insufficient number of useful SSR molecular markers hinders current genetic research in this species. We performed transcriptome sequencing of samples D. cercidifolius var. Longipes using Illumina HiSeq4000. After assembling of transcriptome sequences, a total of 32325 uni-genes were obtained. There were 13779 SSR loci identified using MISA, and the occurrence frequency of SSR loci was 42.63%. The distribution frequency of SSR was 1/2.95kb. The di-nucleotide repeat motif was the most abundant among different repeat motifs, accounting for 44.10% of the total number of repeat motifs. Mono-nucleotide and tri-nucleotide repeat motifs accounted for 37.90% and 16.71%, respectively. The AG/CT was the most abundant di-nucleotide repeat motifs, while the AAG/CTT was the most abundant tri-nucleotide repeat motif, followed by ATC/ATG, ACC/GGT, and AGC/CTG. 60 pairs of random-selected primers were used to test its availability in the random sample of 8 unrelated individuals from different populations using agarose electrophoresis. 46 pairs primers amplified with clear target bands, while 30 pairs were found to be polymorphic using TP-M13 -SSR technology. The amplifying rate and proportion of polymorphic loci were 76.67% and 65.22%, respectively. The results showed that the polymorphism of SSR loci developed based on the transcriptome sequences is higher. The large number of SSR markers in this study should be used for the study of population genetics and phylogeny of D. cercidifolius var. longipes, and provide the referential method of SSR developing for other species.