Abstract: Quasipaa spinosa,so as to provide appropriate molecular markers for the innovative ways of germplasm resource application.【Method】Total RNA was extracted from liver,muscle and kidney tissues of Q. spinosa to build a TRlzol kit. cDNA library and then the library was high-throughput sequenced by the Illumina HiSeq 2500 sequencing platform. Microsatellite searching software MISA was used to screen and analyze microsatellite(SSR)in the Q. spinosa transcriptome while the software SAMtools and VarScan v. 2.2.7 were used for searching SNP loci.【Result】 93887 non-redundant unigenes with a total sequence length of 91352712 bp were obtained from the transcriptome sequencing of Q. spinosa,and all transcriptome Q30 were over 95.00%. Among the 93887 unigenes,33019 potential SSR markers were identified and 21966 unigenes contained SSR loci. In additional,a total of 6688 unigenes had more than one SSR locus. The dinucleotide was the highest at 25788 and the frequency of occurrence frequency was the highest at 27.47%. The average length of SSR was 35.47 bp.(A/T)n was the absolutely dominant repeat motif of Q. spinosa SSR,accounting for 65.51% of the total SSRs,followed by(C/G)_n,(AT/AT)_n,(AC/GT)n,(AG/CT)_n,(AAT/ATT)_n,and accounting for 12.59%,5.66%,5.55%、3.31%,1.55% and 1.30% of the total SSRs,respectively. Among the 33019 potential SSR markers,the times of repetition was mainly between 5-25 times,accounting for 99.91% of the all SSRs. In additional,only 1633 located in the coding area. 17244 SSR loci whose length ≥ 12 bp accounted for 58.53% of the total SSR loci. 120 pairs of SSR primers were selected to verify the validity of the primers and 57 pairs of primers amplified a single band,and the band size was as expected. 87634 SNPs were identified(56300 transitions and 31334 transversions) from mapping sequencing reads to assembled unigenes,the transition/transversion ratio was approximately1.80 and the frequency of base transition is higher than that of transversion.【Conclusion】High-throughput transcriptome sequencing is a feasible method to develop SSR and SNP molecular markers,which can develop molecular markers with universality, large number and wide coverage. Q. spinosa has a moderately high genetic diversity,so it can be used as germplasm materials for further development and utilization.