AbstractChromatin is the genetic material assembled by nucleic acids (including DNA and RNA) and proteins. The biological functions of chromatin are highly dependent on the interaction between DNA (and/or RNA) and proteins that bind to it. Chromatin immunoprecipitation (ChIP) is a powerful technique for evaluating these interactions and has been widely used to characterize the functions of nuclear proteins. However, its application in identifying plant organellar chromatin‐binding proteins is lagging. This article describes the method for analyzing the association of chloroplast‐localized proteins with the chloroplast genome. © 2022 Wiley Periodicals LLC.Basic Protocol 1: Chloroplast isolationBasic Protocol 2: Crosslinking of DNA–Protein complexesBasic Protocol 3: Chromatin isolation and preparationSupport Protocol: Bead‐antibody complex preparationBasic Protocol 4: Immunoprecipitation and washesBasic Protocol 5: DNA preparationBasic Protocol 6: Analysis of results