To develop SSR markers for targeted genes in Badam（Amygdalus communis L.）,this study was based on high-throughput RNA-seq data of Badam leaves,and 41,849 unigenes were assembled,of which 22,894 unigenes were annotated.A total of 5,260 SSR sites were detected from 4,862 unigenes by using MISA.The dominant repeat motifs were single nucleotides（14.30% of the total SSR sites）,followed by dinucleotides（47.64%） and trinucleotides（31.35%）.The most frequent type of dinucleotide repeat motif is AG/CT（22.83%）,and AAG/CTT repeat type in the trinucleotide repeat motif is the most（3.83%）.According to the unigene annotation and KEGG pathway analysis,13 functional genes containing SSR markers associated with lipid synthesis,fatty acid synthesis,seed size and grain weight were discovered,48 pairs of targeted gene SSR primers were designed.The validity of these SSR primers were verified using genomic DNA of Badam leaf,and 33 pairs of primers amplified the clear bands.These SSRs will provide effective targeted gene markers for genetic diversity analysis,molecular-assisted breeding and association analysis of fruit quality traits of Badam germplasm.