Abstract: Compared with SSR markers derived from genomic DNA,the EST-derived SSR markers have remarkable advantages,such as simpler development,greater information and high transferability.In this study,11240 flax ESTs were screened and 877 SSRs were mined out,accounting for 7.8% of the ESTs.Trinucleotide motifs were most abundant(60.1%),followed by dinucleotides(21.9%).The AGA/TCT,GA/CT,AAG/TTC,TC/AG,and TA/AT motifs were themain repeat types,accounting for 6.2%,6.2%,5.9%,5.8% and 5.8% of the 877 SSRs respectively.Tetra-,penta-and hexa-nucleotide motifs represented 18% of the SSRs identified.Seventy-three primer pairs were designed from the SSR containing ESTs,and PCR amplifications were performed among eight flax cultivars.Sixty-three primer pairs yielded amplification products,accounting for 86.3% of the total primers.Polymorphisms among the eight cultivars were found in 17 primer pairs,accounting for 26.3% of the primers with amplification products.