DNA methylation is one of the most important and common modifications in epigenetics.With progress of the studies on DNA methylation,methylation-sensitive amplified polymorphism（MSAP）,which is developed from AFLP technology and basing on the PCR technology,has been a effective means for detecting DNA methylation levels because of its wide range of applications and simple of operation.It has been widely applied to many fields currently,such as germplasm identification,variety improvement and regulation of gene expression.In this paper,the principles and operational processes of MSAP technology and applications of MSAP in maize genetics and breeding were summarized.Also the future of applications prospects of MSAP technology was carried out.