Prevention of autonomous egg division before fertilization ensures successful reproduction in flowering plants. The double fertilization triggers the initiation of embryogenesis and endosperm formation. The molecular mechanism that prevents the initiation of embryo and endosperm is not well understood. Here we show in rice (Oryza sativa) that the FIS-PRC2 homologous genes rice FERTILIZATION INDEPENDENT ENDOSPERM 1 (OsFIE1) and OsFIE2 redundantly repress egg and central cell respectively from autonomous division. Ovules with the Osfie1 and Osfie2 double mutations caused parthenogenesis and autonomous endosperm formation at very high frequency, while the single Osfie2 mutation resulted in pre-embryo-like structure formation from synergids at a low frequency without fertilization. The transcriptomic results indicate that the maternal alleles of the usually paternal genome expressed pluripotency factors were activated, suggesting that the FIS-PRC2 may repress the pluripotency factors directly in egg before fertilization. Similarly, the maternal alleles of the paternally expressed imprinted genes (PEGs) were activated in the autonomous endosperm, including the conserved auxin biosynthesis imprinted gene OsYUCCA11, consistent with our ChIP assay where PRC2 modulated H3K27me3 targets the maternal alleles of PEGs in endosperm. The identification of the FIS-PRC2 function in repressing autonomous division of egg and central cell in rice shed light on how epigenetic regulation and fertilization interplay to ensure proper seed development. The function of FIS-PRC2 may be manipulated for inducing haploid for speed breeding or harnessed for engineering synthetic apomictic crops.