Histone H3 lysine 9 and lysine 27 are two important targets for epigenetic modifications in plants. H3K9 methylation is either associated with heterochromatin formation or gene repression, while H3K27 methylation profile is likely to be involved in gene expression required for developmental decisions. Although a number of modification enzymes are being identified, the mode of action and functional interplay between the histone modification enzymes and other chromatin pathways remain largely unknown. Studying the regulatory mechanism of histone H3K9 and H3K27 modification would provide important clues to reveal the molecular basis of establishment, inheritance and erasure of epigenetic information during plant cell division and differentiation.