Abstract:In this investigation, the levels and patterns of DNA methylation of common wheat Chinese Spring (CS) and CS-2C gametocidal chromosome monosomic addition line (CS-2C) were identified using MSAP method, to explore the relationship between the DNA methylation and the gametocidal chromosome. The results show that, cytosine methylation level of CS-2C monosomic addition line 5 ‘-CCGG sites (45.33%) was higher than that of CS (40.35%), the full methylated rate and hemi-methylated rate were increased. Obvious variation of cytosine methylation at 5‘-CCGG sites was detected, in which CG methylation variation range was higher than that of CHG methylation variation. After collecting and sequencing the differentially methylated DNA fragments some of fragments homologous with Carazinho transposon Sukkula-like etc were found. It can be proposed that transposons may play a role in gametocidal mechanism. The purpose of this study was to reveal the molecular mechanism of gamtocidal chromosome.