A prominent positive magnetic anomaly spans the 100 km distance between Prince Edward Island and Cape Breton Island in the southern Gulf of St. Lawrence. The anomaly occurs in an area of complex structure where Appalachian terrane boundaries are poorly resolved because of thick late Paleozoic sedimentary cover. Analysis of the magnetic anomaly led to the interpretation that it is produced by four separate, approximately circular, source bodies aligned along the northwesterly trend of the anomaly. Seismic data, physical property measurements, and magnetic and gravity anomalies were used to further investigate the anomaly sources through forward modeling techniques. The four source bodies have densities and magnetic susceptibilities compatible with dioritic to granitic compositions. Modeling also suggests that basement to the north of the plutons has higher density and susceptibility than basement to the south, and hence the source bodies are interpreted as plutons emplaced along the boundary between Ganderian composite terranes to the north and the Ganderian Brookville – Bras d’Or terrane to the south. This interpretation suggests that the Ganderia–Avalonia boundary is located farther south, and shows the need for re-evaluation of the location and role of the Canso fault in offsetting terranes between Cape Breton Island and southern New Brunswick.