DNA methylation, the most common DNA modification in eukaryotes, is an important component in epigenetics and plays essential roles in the regulation of gene expression, resistance to biological stress, growth and development in plant. With progress in study on DNA methylation, methylation-sensitive amplified polymorphism （MSAP） is an AFLP-hased technique with high-throughput, superiority of generating abundant polymorphism profile, low cost and easy operation for detecting status of DNA methylation. Currently, it has been widely applied in the various fields of plant genetics research. In this paper, the principles, procedures, and application of MSAP in plant genetic studies were summarized. At the same time, the perspective of its application in the future was discussed.