PlantEMS (Plant Epigenetic Modification Sites) is an integrative database for storing, analyzing and visualizing of DNA, RNA, and protein PTM (post-translational modification) sites in plant. The PlantEMS provides the experimental-confirmed modification datasets in 54 plants from published literatures and databases. In total, 13,009,568 DNA modification sites for 4 types, 33,337 RNA modification sites for 28 types, and 132,232 PTM sites for 25 types are collected and integrated in the PlantEMS. The PlantEMS will become a powerful tool to offer a comprehensive view of epigenetic modification in plant.