DNA methylation is known to play a crucial role in regulating plant development and or- gan or tissue differentiation. In this study, we as- sessed the extent and pattern of cytosine methylation during rapeseed (Brassica napus L.) seed germina- tion, and compared the methylation level of various tissues in seedling, using the techniques of methyla- tion-sensitive amplified polymorphism (MSAP) and HPLC separation and quantification of nucleosides. In all, 484 bands, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified by 12 pairs of selective primers in DNA ob- tained from dry seeds. A total of 76 sites were found to be differentially digested by the isoschizomers, indicating that approximately 15.7% of 5′-CCGG-3′ sites in the genome were cytosine methylated. Four classes of patterns were observed in a comparative assay of cytosine methylation in the dry and germi- nating seeds; a small number of hypermethylation events occurred at 5′-CCGG-3′ sites in germinating seeds compared with dry seeds, while many more hypomethylation events were detected after seed germination. Differences in DNA methylation level in various tissues were also detected; radicel was less methylated than hypocotyl and cotyledon. These observations were further confirmed by HPLC analy- sis. In addition, sequencing of eleven differentially methylated fragments and the subsequent blast search revealed that cytosine methylated 5′-CCGG- 3′ sequences were equally distributed between cod- ing and non-coding regions. These results clearly demonstrate the power of MSAP technique for large-scale DNA methylation detection in rapeseed genome, and the complexity of DNA methylationchange during seed germination. DNA Hypomethyla- tion going with seed germination appears to be a necessary step toward transcriptional activation in gene expression, and may well contribute to the de- velopmental gene regulation. In this study, we as-sessed the extent and pattern of cytosine methylation during rapeseed (Brassica napus L.) seed germina- tion, and compared the methylation level of various tissues in seedling, using the techniques of methylase-sensitive amplified polymorphism (MSAP) and HPLC separation and quantification of nucleosides. In all, 484 bands, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified by 12 pairs of selective primers in DNA ob- tained from dry seeds. A total of 76 sites were found to be differentially digested by the isoschizomers, indicating that approximately 15.7% of 5’-CCGG-3 ’sites in the genome were cytosine methylated. Four classes of patterns were observed in a comparative assay of cytosine methylation in the dry and germi-nating seeds; a small number of hypermethylation events occurred at 5 ’ -CCGG-3 ’sites in germinating seeds compared with dry seeds, while many more hypomethylation events were detected after seed germination. Differences in DNA methylation level in various tissues were also detected; radicel was less methylated than hypocotyl and cotyledon. These observations were further confirmed by HPLC analy- sis. In addition, sequencing of eleven differentially methylated fragments and the subsequent blast search revealed that cytosine methylated 5’-CCGG- 3 ’sequences were equally distributed between cod- ing and non-coding regions. These results show demonstrate the power of MSAP technique for large-scale DNA methylation detection in rapeseed genome, and the complexity of DNA methylation change during seed germination. DNA Hypomethylation going with seed germination appears to be necessary step toward transcriptional activation in gene expression, and may well contribute to the de- velopmental gene regulation