The island of Mozia represents a unique location for geophysical investigations applied to archaeological research. The presence of exposed structures and ongoing studies, run by the University ‘La Sapienza’ of Rome, allows a direct comparison of geophysical exploration data with the excavations results, giving an immediate control on the accuracy and robustness of the geophysical survey conducted. Four areas around the Kothon, a Phoenician artificial basin, have been investigated by means of magnetic methods; the purpose was to trace a semi-circular wall surrounding the structure of the basin. The geophysical results confirmed the presence of the wall, as postulated by the archaeological study, and indicated magnetic anomalies associated with previously unknown structures. Subsequent archaeological excavation confirmed these latter data. The magnetic signature of the topsoils and remains characterizing the area surveyed,was undoubtedly weak, even though the resulting anomalies maps were adequately clear and allowed the characterization of the archaeological structures in the area. Field and laboratory magnetic susceptibility measurements allowed better understanding of the data. The study confirmed that geomagnetic investigations can be used in weakly magnetic susceptibility environments, as in Mozia, and are productive if conducted in accordance with an archaeological agenda. Copyright © 2011 John Wiley & Sons, Ltd.