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The present work focuses on the study of the main ophiolite complex of Northern Greece, which is one of the dominant geological features in the broader Aegean area, by the use of geophysical (gravity and magnetic) data. This ophiolite complex, which trends in a NW-SE direction, starts at the eastern part of the borders of Greece with F.Y.R.O.M. and continues up to the southern part of the Chalkidiki Peninsula. The ophiolites mainly consist of dense, high-susceptibility peridotitic and gabbroic rocks. As a result, the southwestern part of the ophiolitic complex, which crosses the northwestern part of the Chalkidiki-Peninsula, gives rise to both high amplitude aeromagnetic and Bouguer anomaly values. On the other hand, the Axios-Thermaikos basin, which is situated at the western border of the ophiolitic complex, exhibits a deep sedimentary cover that results in low Bouguer anomaly values. The corresponding Bouguer anomaly decreases to the southwest, indicating an increase of the sedimentary layer thickness in that direction.2.5-D inversion was applied to both the aeromagnetic and the Bouguer gravity data along several profiles. All the profiles were oriented normal to the main trend of the ophiolitic complex. Information from two deep boreholes, as well as the surface occurrence of the ophiolites was used as constrains to the inversion scheme. The produced model shows an average sedimentary thickness of 2.5 km along the coastline. From the joint inversion of the Bouguer and aeromagnetic anomaly data the existence of two ophiolitic stripes is revealed. The first “external” one is located in the southwest part, while the other “internal” one to the northeast part of the belt. In the internal one, the depth extent of the ophiolites was estimated to range between 1 to 4 km. Moreover, the ophiolites were found to dip towards the northeast, but their dip varies from 20–45° in the northern part to 10–15° in the southern part of the stripe. For the “external” stripe the extent of the ophiolitic bodies varies from northwest to southeast, reaching its highest depth of 5 km to the south. This stripe is also dipping towards the northeast with a dip of 10–15°.