Abstract: To find out the relationship between DNA methylation and chemical components in flue-cured tobacco,the DNA methylation DArT chip of flue-cured tobacco was used in analyzing the DNA methylation and chemical components in leaves sampled from three stalk positions of cv.K326,Honghuadajinyuan and Zunyan 6 at different development stages in Guiding and Xingyi.The results showed that the DNA methylation level of flue-cured tobacco varied widely from 35.4% to 64% with the average level of 47.61%.The difference of methylation mode was bigger between tobacco cultivars,than that between stalk positions.The correlation analysis of DNA methylation with the activities of 12 enzymes key to substance metabolism and 76 aromatic chemical components indicated that their correlation was extremely significant(p<0.01),there were 34 significantly correlated chemical components/enzymes(p<0.0001) existed in the three tobacco cultivars in common,and special regulated chemical compounds were also existed in different cultivars.