Abstract: To investigate the DNA methylated modification levels，patterns and sites of the Ginkgo biloba at the genome-wide level，the double digestion of EcoRⅠand HpaⅡ/MspⅠwas used to construct the Ginkgo biloba genomic MSAP（methylation-sensitive amplification polymorphism，MSAP）analysis system. By using 16 pairs of selective primers from the 54 pairs of MSAP selective primers，a total of 454 legible and repeatable amplified DNA bands were detected，on average 28.38 bands were observed after amplification with each primer pair. Two-hundred DNA methylated sites were detected among all the amplificated sites，which represented 44% ratio of methylated modification at CCGG/GGCC sites in Ginkgo biloba genome. Eighteen methylated DNA sequences were isolated and sequenced by extracting part of the amplificated sites. BLASTn comparison indicated that the DNA methylated modification phenomenon was existed in multiple types of DNA sequences，including repeated sequences，transcription regulators，retrotransposons，channel protein，promoter-binding protein，protein kinase，etc.

Key words: Ginkgo biloba, epigenetic, DNA methylation, methylation-sensitive amplification polymorphism