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For more than a decade now, geophysical prospecting has been considered an integral part of archaeological research; the ability to quickly investigate large areas and locate objects buried in the ground without directly interacting with it is a key feature that makes such surveys essential for identifying and locating, with good accuracy, buried archaeological remains. In this study, two extensive magnetic and electromagnetic surveys were carried out in two different areas of the Akrai archaeological site, where given the distribution of archaeological remains already found at the site, it was likely that additional buried remains were present. The surveys were performed using a proton precession magnetometer and a multifrequency electromagnetic device with a frequency range of 2.5–250 kHz. By processing the data, the vertical magnetic gradient and electrical conductivity maps were obtained. Furthermore, 3D models of electrical conductivity distribution were reconstructed. On comparing the results, it was notable that many anomalies characterized by low vertical gradient values were identified within areas characterized by low electrical conductivity values. These anomalies detected by both surveys can be associated with good probability with buried archaeological remains made up of limestones. In fact, they exhibit shapes and sizes comparable to those of the wall remains already found at the site.