Epigenetic control of plant development via histone modifications is involved in different processes ranging from embryonic development, vegetative development, flowering time control, floral organ development, to pollen tube growth. The identification of an increasing number of epigenetically regulated processes was greatly advanced by methods allowing the survey of genome-wide histone modifications and chromatin-protein interactions. However, genome-wide approaches are too broad to access in detail a large number of histone modifications taking place at a single locus. Here, we provide a robust chromatin immunoprecipitation (ChIP) protocol, allowing in vivo analyses of multiple chromatin modifications and binding of histone modifiers in different plant organs and tissues. This method is quantitative and provides a way to study the dynamic state of chromatin during plant development and also in response to different environmental stimuli.