Abstract: miRNA target identification has been one of the study hotspots in plants. Recently, a high-throughput technique known as degradome sequencing has made it possible to sequence mRNA cleavage products on a large-scale. Computational methods now exist to use these data to find targets of conserved and newly identified miRNAs. This technology has been applied to study the regulation modes of miRNAs on their target genes during plant growth, development and environmental stress responses. In this paper, the protocols, analysis tools and application examples of degradome sequencing in plants were reviewed to provide useful knowledge background for studying gene regulation network.