Based on MSAP system,we investigated the potential relationship between genomic DNA methylation variation and arris variation of in vitro pitaya (Hylocereus undatus ‘Zihonglong’) shoots.DNA methylation levels and patterns were detected under different subculture duration and cycles using MSAP marker.Also,the relationship between exogenous GA concentration (0,1.5,3.0,4.5,and 6.0 mg/L),endogenous GA content and DNA methylation variation were illustrated.The results showed that no significant correlation was observed between arris and DNA methylation variation.DNA methylation levels of in vitro shoots increased along with the elongation of culture time and subculture cycles.The ratio of semi-methylation in external cytosine were firstly reduced,followed by an increase,which was somewhat consistent with variation of endogous GA contents (406.7,424.3,440.6,398.6 and 409.1 pg/mL).Ratio of full methylation in internal cytosine of CCGG sites demonstrated a negative correlation with the change of ratio in external cytosine,indicating that,exogenous GA might considerably influence the accumulation of endogenous GA.Furthermore,different forms of methylation patterns might be converted to each other,and thus remained the stability of total DNA methylation level.Along with the increase of the exogenous GA concentrations,the mutation rate of DNA methylation decreased (3.6%→4.5%→3.1%→2.7%),which revealed that,DNA methylation variation of pitaya was more sensitive to low GA concentration.