Histone lysine methyltransferases (HKMTs) are key mediators of epigenetic silencing. Our previous work demonstrated a critical role for the H3K27MT EZH2, the catalytic subunit of the Polycomb repressive complex 2 (PRC2), for the maintenance of HIV-1. In this study, we showed that depletion of individual subunits of PRC2 by shRNA partially reactivated and sensitized latent HIV-1 proviruses to exogenous stimulations in latently infected Jurkat T-cell lines. Chromatin immunoprecipitation (ChIP) experiments demonstrated that PRC2 and G9a were highly enriched at proviral 5′ LTR and rapidly displaced upon TNF-α reactivation. Depletion of EZH2 expression by shRNA in Jurkat T cells or inhibition of EZH2 methyltransferase activity in primary T cells before HIV-1 infection significantly reduced levels of silent viruses. Similarly, shRNA depletion of G9a or inhibition of its enzymatic activity by UNC0638 prior to HIV-1 infections also resulted in decreasing of silent viruses. In addition, inhibition of EZH2 enzymatic activity by GSK-343 or EPZ-6438 in resting memory T cells cultured ex vivo or isolated from HIV-1 infected patients receiving highly active antiviral therapy (HAART) caused spontaneous reactivation of latent proviruses. Treatment of resting memory T cells isolated from HIV-1 infected patients with UNC-0638 also partially reactivated latent proviruses, even though shRNA depletion of G9a had relatively little impact on reactivation of latent proviruses in Jurkat T cells. We conclude that both PRC2 and G9a are required for the establishment and maintenance of HIV-1 proviral silencing in primary cells. Furthermore, HK3MT inhibitors, such as GSK-343, EPZ-6438 or UNC-0638, are highly potent as latency-reversing agents (LRAs) when combined with other agents to reactivate latent HIV-1 ex vivo.