Abstract: To study the genetic diversity and genetic linkage mapping of Taxus chinensis var. mairei without information of the whole genome，the SSR primers were designed based on the transcriptome data （from NCBI）from roots，stems and leaves of 13 737 528 reads were assembled into 96 279 unique sequences with 38 Mb total nucleotides，in which 2 160 SSRs（2.24%）were identified，with the average frequency of 1/18.01 kb and the motifs length of 14 to 25 bp，by using SSR finding soft. Hexunucleotides （38.56%）and trinucleotides（37.08%）appeared to be the most abundant repeated motifs. Seven hundred and three repeat motifs were composed of 2 160 SSRs，in which hexunucleotides were accounted for 60.96%，with the repeat frequency of 3 to 4 times. Among the dinucleotide and trinucleotides SSR motifs（44.81%），the most abundant was（AG/CT）_n，（AT/AT）_n，（AAG/CTT）_n，（AGC/CTG）_n，（AGG/CCT）_n and（ATC/ATG）_n accounting for 34.73% of the total SSRs. A small amount of repeats were（CG/CG）_n and（CCG/ CGG）_n the optical amplifications were performed in 10 μL final volume containing 20 ng DNA，1× PCR buffer（Tiangen），20 mmol MgCl₂，0.35 mmol each of dNTPs，0.25 μmol each of primers，0.45 U polymerase Taq（Tiangen），according to the orthogonal test of L₉（3⁴）. Sixty-two potential markers sites were randomly selected to validate the assembly quality and develop SSR markers. Among 8 Taxus germplasms，effective PCR success rate and polymorphism rate of 62 markers were separately 53.23% and 38.71%. This study is important for analyzing genetic diversity，marker assisted selection，genetic linkage mapping and functional gene mining of Taxus chinensis var. mairei by using SSR molecular markers.

Key words: Taxus chinensis var. mairei, transcriptome, primer, SSR