Genomic imprinting is an epigenetic phenomenon causing parental alleles to be active depending on their parent-of-origin. In plants, imprinted genes are mainly confined to the endosperm, an ephemeral tissue supporting embryo development. Differential methylation of histone H3 on lysine 27 (H3K27me3) established by the Polycomb Repressive Complex 2 (PRC2) is a major regulatory mechanism determining activity of paternally expressed imprinted genes (PEGs) in animals and plants. Here, we show that the coding region of many PEGs is marked by an epigenetic signature of H3K27me3, H3K9me2 and CHG methylation and that the combination of these three modifications correlates with paternally-biased gene expression in the endosperm. The maternal alleles of PEGs are marked by CHG methylation in the central cell, indicating that the repressive epigenetic signature of PEGs is established before fertilization. We use the presence of the three modifications to predict novel PEGs and propose that genomic imprinting is substantially more common than previously estimated based on expression data. Overall design: Col × Ler reciprocal crosses were performed using Arabidopsis lines expressing PHE1::NTF and PHE1::BirA. 4DAP siliques were collected and tissue homogenization and nuclei purification were performed from three biological replicates for LerxCol and two for ColxLer using INTACT. Total RNA was extracted from purified nuclei using the mirVana Isolation Kit Protocol (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation and the Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit from Illumina. Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.