Though big and fertile, the island of Paros is still an empty landscape for the Neolithic, since alone the only so far known site of Kastro at Paroikia, and the neighbouring islet of Saliagos are inadequate to give an overall view of the cultural and economic distribution of the Neolithic populations on the island and their site networks within it. Also, even in the EBA, the few so far located settlements compared to the known cemeteries prevent us from penetrating into the subsistence strategies of the EC people and their organization of everyday life. In this respect the location of Neolithic and EBA habitation deposits at two sites in the bay of Naousa, Koukounaries and Sklavouna, is a significant opportunity for prehistoric research. This paper is a preliminary synthesis based on data from the old (1974–91) excavations and the systematic study started recently. Particularly in regard to Koukounaries, the paper attempts to study the organization and distribution of the pre-Mycenaean populations on the hill per chronological phase, giving emphasis on two main issues: first, on the duration of the latestNeolithic phase and the possibility that a Neolithic-to-EBA transition exists at the site, and secondly on the presence of a significant stone building compound of the EC II at the NE fringe of the hilltop.