Abstract: In this study，a total of 68 998 Unigenes from transcriptome of Clausena lansium were used for screening of SSR loci using MISA software. 11 825 SSRs，including the types of 1–6 nucleotide repeats distributed in 11 000 Unigenes were identified，with occurring frequency of 17.14% and mean distance of 4.41 kb. The major types of SSR loci were 1–3 nucleotide repeats，accounting for 93.93% of the SSR loci，of which mono-，di- and tri- nucleotide repeats were 41.48%，24.92% and 27.53%，respectively. Two hundred and seven repeat motifs with iteration numbers from 4 to 24 were discovered from the 11 825 SSR loci，and the most abundant motif were A/T，AG/CT，AT/AT，AAG/CTT and AAT/ATT. The lengths of repeat nucleotide sequences for all SSR loci ranged from 12 to 25 bp，with most from 12 to 15 bp，accounting for 50.95% of all SSR loci. A total of 6 102 SSR primers were designed and 30 primers were selected randomly for PCR amplification tests，of which 24 primers amplified effective and 13 primers showed polymorphism in sixteen different wampee germplasm. The results indicated that the Unigenes generated from trasncriptome sequencing in C. lansium could be used as an effective source to develop SSR markers. The large quantities of SSR markers will provide reliable markers for map structure，genetic polymorphism analysis for wampee germplasm resource.

Key words: Clausena lansium, transcriptome, SSR, usability analysis