DNA methylation is one of the epigenetic phenomena which can be transferred to the offspring by cell division in the evolution of organisms.The epigenetic regulation accompanied by gene expression can be found directly in the phenotype of haploidy plants.DNA cytosine methylation at the 5’-CpCpGpG sites of haploid,Shuhui 527,Shuhui 363 and their hybrids was analyzed by methylation sensitive amplification polymorphism(MSAP) method.There were 765 DNA methylated sites detected and the methylation level was lower in hybrids than parents.Meanwhile,the different bands between hybrids and parents were analyzed and two types of methylated sites were detected,of which one inherited from haploid,and the other did not.The biological functions of genes related to methylated sites involved in cell structure,metabolize and response factor.Therefore,DNA methylated modifications can activate and silence the genes and play an important role in plant growth,development and evolution. DNA methylation is one of the epigenetic phenomena which can be transferred to the offspring by cell division in the evolution of organisms. The epigenetic regulation accompanied by gene expression can be found directly in the phenotype of haploidy plants. DNA cytosine methylation at the 5’- CpCpGpG sites of haploid, Shuhui 527, Shuhui 363 and their hybrids were analyzed by methylation sensitive amplification polymorphism (MSAP) method. There were 765 DNA methylated sites detected and the methylation level was lower in hybrids than parents. During this, the different bands between hybrids and parents were analyzed and two types of methylated sites were detected, of which one one inherited from haploid, and the other did not. The biological functions of genes related to methylated sites involved in cell structure, metabolize and response factor.Therefore, DNA methylated modifications can activate and silence the genes and play an important role in plant growth, development and evolution.