No reports have examined the association between tamoxifen resistance and the methylation of the estrogen receptor (ER) alpha and beta genes. Therefore we investigated the methylation patterns of the ER genes in the tamoxifen-resistant tumors. We used bisulfite genomic sequencing and reverse transcriptase PCR to determine the methylation patterns and mRNA expression of the two ER genes from control (n = 68) and tamoxifen-resistant tissues (n = 34) chosen by an age-matched sampling method. Bisulfite genomic sequencing allowed us to reveal the methylation of the ER alpha gene in 15 of the control tumors (22.1%) and in 11 tumors of the resistant group (32.4%). The methylation of ER beta was observed in 40 control tumors (58.8%) and in 8 recurrent tumors (23.5%). The methylation rate of the ER beta but not the ER alpha in the control group was significantly higher than in its counterpart (ER alpha, P = 0.261; ER beta, P = 0.001). Among the methylated tumors mean methylation density of ER alpha and ER beta in the resistant cases was significantly elevated (ER alpha, P = 0.014; ER beta, P < 0.001). Furthermore, the expression rate of ER beta mRNA was higher among the tumor in the resistant group than in the control with marginal significance (77.8% vs. 38.1%, P = 0.109). Additionally, in the cancers from the resistant cases, the cells showed a higher percentage of positive staining for Ki67 than those from the control group (P = 0.001). Our study indicates that there is an inverse relationship between the methylation rate of the ER beta gene and tamoxifen resistance. The tamoxifen-resistant tumors showed more dense methylation of the ER beta gene than control tumors. Although the number of case samples was limited, our results support the hypothesis that hypermethylation of the ER beta gene negatively affects the development of tamoxifen resistance.