design: Astragalus membranaceus is an important medicinal plant widely cultivated in East Asian. microRNAs (miRNAs) are endogenous regulatory molecules that play essential roles in plant growth, development, and environmental stress response. Recent transcriptome studies in A. membranaceus have provided a large number of nucleotide sequences and identified a larger batch of genes which provided basis for further molecular genetics study. However, miRNAs and miRNA targets from A. membranaceus remain unknown. To identify miRNAs and their target genes in A. membranaceus, high-throughput sequencing technology using Illunina high throughput platform was conducted followed by bioinformatics analysis.