Abstract: To test the feasibility of bisulfite sequencing in methylation analysis at a specific gene of rice,we analyzed DNA methylation at fragment of CpG island of FIE2A.In the present paper,genomic DNA was extracted from leaf and endosperm of rice with the CTAB method.After treated with bisulfite sodium,we amplified the CpG island of FIE gene with designed primers using nest-PCR,sequencing results after cloning in TA-vector.Results showed that nest-PCR increased the specificity of the PCR products,and symmetric sequences of CG,CNG were hypermethylated,whereas asymmetric sequences of CNN were hypomethylated.Wild leaf displayed a high average level of methylation.Our results indicated that bisulfite sequencing could be used in analysis of methylation at CpG island of specific genes in rice.