A total intensity survey of the large magnetic anomaly in the Berchtesgaden area in the Northern Calcareous Alps has been carried out. The anomaly can be simulated by two-dimensional plate-like bodies having a NS extension of about 65 km, lower boundaries between 20 and 10 km and upper boundaries up to 5 km below the surface, depending on the intensity of magnetization (1–2 · 10−3 G). A comparison with Bouguer gravity data favours a relatively thin magnetic source layer with a lower boundary at about 10 km and an upper boundary at about 5 km. From the magnetization required for modelling it can be concluded that mafic and possibly also ultramafic rocks are the causes of the anomalies. Two interpretations are suggested: 1) The magnetic source layers could form part of the metamorphic complex of the Bohemian Massif, belonging to a paleo-European plate. There would be probably no relation to the processes involved in the formation of the Alps in this case. 2) The magnetic source layers could be part of an ancient tethyan ocean floor, and should then be considered in relation to fossil subduction zones proposed in different models for the geodynamic evolution of the Eastern Alps.