Chatzimarkakis has been a member of the European Parliament since July 2004 for the FDP party of Germany. In the 2014 European Parliament elections he stood for the newly formed Greek party Greek European Citizens. He currently sits on the European Parliament's Committee on Fisheries as well as on the Committee on Budgetary Control, for which he is a coordinator. He also chairs the Delegation of the European Union to the Republic of Macedonia. He is a supporter of the Spinelli Group.