Examining the relationship between the Aeginetans and Kydonia and the role of the former in the shaping of the political and economic situation in Western Crete, and considering Cross’s (2011) theory on the relationship between Lachania and Kydonia and Sekunda’s (2000) theory on the Federation of the Polichnitans as a union of small hinterland communities inhabited by indigenous Kydones, the paper attempts: a) to identify the site at Kastelos, Varypetro, 8 km south-southwest of Chania (ancient Kydonia) as the administrative center of the Federation of the Polichnitans, and b) to explain the conflict between Kydonia and the Polichnitans as the result of political and ethnic disputes between the Kydonians and the Polichnitans/Kydones as well as a conflict of financial interest between Kydonia and Gortyna with respect to the mountainous hinterland of western Crete and trade routes to the Libyan Sea.