We carry out a study to analyze the relation between polymorphisms of GSTT1, GSTM1 and the capacity of arsenic methylation in a human population exposed to arsenic in drinking water. 230 randomly chose subjects were divided into four subgroups based on the arsenic levels, and then the associations between the polymorphisms of GSTT1, GSTM1 and methylation of arsenic were investigated. The levels of inorganic arsenic (iAs), monomethylated arsenic (MMA), dimethylated arsenic (DMA) and total arsenic (TAs) in urine were higher in males than that in females. Moreover, the levels of iAs and TAs in urine in the subjects with genotype of GSTM1(+) were significantly higher than those with GSTM1(-); the level of DMA in the subjects with GSTT1(+) and GSTM1(+) were higher than those with GSTT1(-) and GSTM1(-), although it is not statistically significant. Secondary methylation index (SMI) was significantly higher in the subjects with genotype of GSTT1(+) than those with GSTT1(-). The levels of TAs in urine, together with the genotypes of GSTT1/GSTM1 were associated with the levels of MMA and DMA. Our results suggested that the polymorphisms of GSTT1 and GSTM1 were associated with the methylation of arsenic, especially the levels of DMA and SMI.