Abstract: Forty-five thousand six hundred and fifty-six unigenes from fruit transcriptome of Lonicera caerulea L. were screened using MISA software. A total of 14 841 SSRs that occurred in 11 251 unigenes were identified，and the frequency of these SSRs was 32.51% and mean distance was 2.58 kb in the unigenes. Mononucleotide，dinucleotide and trinucleotide were major types，accounting for 34.81%，42.79% and 20.64%，respectively. The dinucleotide repeat motifs of AG/CT were the predominant repeat types（27.2%）. The trinucleotide repeat motifs of AAG/CTT were the predominant repeat types（6.18%）. Twenty-one thousand eight hundred and sixty-seven pairs of SSR primers were designed using Primer 3.0. Randomly 20 pairs of primers were selected for PCR amplification，8 amplified on clear and reproducible bands，5 in 16 different types showed polymorphism in materials. Sixteen plants were divided into 3 groups by UPGMA. Abundant SSR polymorphisms provide more reliable markers for Lonicera caerulea L.fruit genetic diversity analysis and genetic map construction.

Key words: Lonicera caerulea, SSR, transcriptome, polymorphism