An application of magnetic survey to the submerged Roman ruins of the Bay of Baia, volcanic area of the Phlegrean Fields,Naples (southern Italy) is presented and discussed.The site of Baiae, one of the most extensive submerged archaeological sites knownin Italy, is characterized by urban sites with residential houses, thermal baths, fisheries and harbour buildings.The survey was aimed to establish the typical magnetic signatures of building structures submerged in a volcanic marine environment. The comparison of both the maps of the magnetic anomaly field and of the computed analytic signal with the known submerged archaeological structures of the area gave some interesting insights into the lithological characteristics ofthe archaeological structures ofthe Baiae site and showed the effectiveness of the magnetic method for mapping remnants of building structures beneath the sea bed.