Marine magnetic anomalies are traditionally modelled using a constant thickness source layer, usually defined as the extrusive lavas associated with seismic layer 2A. Recent seismic studies reveal that the thickness of layer 2A can vary by more than a factor of two, an observation which has important implications for the magnetic anomaly source layer. We model deep-tow magnetometer data from the Endeavor Segment of the Northern Juan de Fuca Ridge, in combination with nearby seismic data and find a positive correlation between the thickness of the seismically-defined layer 2A and the magnetic anomaly source layer. This suggests that short-wavelength magnetic anomalies observed within individual magnetic polarity units can arise from variations in the thickness of the extrusives, rather than geomagnetic field variations or secondary magnetization. ¿ American Geophysical Union 1993