Abstract: DNA methylation was considered to be the best way to study on epigenetic phenomenon of autopolyploid. The levels and patterns of methylation in mulberry were studied based on ‘Shinichinose’, ’Shansang 305’and’Shansang 402’. 21 primers combinations were selected to apply MSAP analysis. 507, 507 and 511 sites were detected respectively in ‘Shinichinose’, ’Shansang 305’and’Shansang 402’. The results showed that the total methylation level had little differences in ‘Shinichinose’,’Shansang 305’and’Shansang 402’ as a whole. The methylation patterns of mulberry had a large amount of adjustment after polyploidization, type B was the most and type C following behind in all types. It is conjectured that the DNA methylation maked the genome double and regulated gene expression to appear the advantages of agronomic traits.