Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of the polycomb repressive complex 2 and suppresses gene expression by catalyzing histone H3 methylation on lysine 27. EZH2 is overexpressed in metastatic prostate cancer and has been shown to promote cell proliferation and metastasis. Here we show that EZH2 also suppresses prostate cancer apoptosis by coordinating the epigenetic silencing of two pro-apoptotic microRNAs, miR-205 and miR-31. We previously reported that miR-205 is silenced in prostate cancer through promoter methylation. In this study, we found that EZH2 suppresses miR-31 expression by trimethylation of H3K27 on the miR-31 promoter. SiRNA knockdown of EZH2 increased miR-31 expression and decreased the anti-apoptotic protein E2F6 (a target of miR-31), resulting in the sensitization of prostate cancer cells to docetaxel-induced apoptosis and vice versa. We further demonstrated that miR-205 silencing is linked to miR-31 silencing through EZH2. Suppression of miR-205 caused an increase of EZH2 protein, which in turn inhibited miR-31 expression and vice versa. Thus, EZH2 integrates the epigenetic silencing of miR-205 and miR-31 to confer resistance to chemotherapy-induced apoptosis. Besides the histone modification by histone methyltransferases (HMTs) such as EZH2, histone deacetylases (HDACs) offer another mechanism to epigenetically regulate gene expressions in cancer. The class I selective inhibitor of HDACs, mocetinostat, has promising antitumor activities in both preclinical studies and the clinical trials. To understand how mocetinostat induces apoptosis in prostate cancer cells, we examined the effects of mocetinostat on miR-31. We found that miR-31 was significantly upregulated by mocetinostat in prostate cancer cells. E2F6 was decreased by mocetinostat treatment. Mocetinostat also increased the expression of pro-apoptotic protein Bad and activated caspase-3 and caspase-9. SiRNA iv knockdown of E2F6 sensitized cancer cells to mocetinostat-induced apoptosis. Importantly, we found the same results in the primary prostate cancer stem cells. Thus, activation of miR-31 and downregulation of E2F6 contribute to mocetinostat-induced apoptosis in prostate cancer. In summary, the epigenetic silencing of miR-31 confers a resistance mechanism for chemotherapy-induced apoptosis in prostate cancer cells. Using mocetinostat to activate miR-31 expression is a novel strategy to overcome resistance to apoptosis and improve response to therapy.