Chatzimarkakis is a member of the national executive committee of the FDP and of the European Liberal Democrat and Reform Party council since 1995. From 2002 to 2010 he was secretary-general of the FDP regional association of the Saarland. He is a founding member of the "Dahrendorfkreis", a wing of the FDP that advocates for sustainable liberalism. After the FDP lost two regional elections in Rhineland-Palatinate and Baden-Württemberg, Chatzimarkakis was one of the main critics of the party leader Guido Westerwelle.