Sea surface, deep tow, and submersible magnetic surveys show that the spreading axis of the Cleft segment of the southern Juan de Fuca Ridge (SJDF) is overlain by a distinctive magnetic anomaly low in contrast to the more typical magnetic anomaly high found over the adjacent Vance segment and most mid-ocean ridge spreading centers. Forward iterative thickness modeling, based on the near-bottom magnetic data, shows that this axial magnetic low can be produced by a thin magnetic source layer beneath the cleft axial valley. Thick crust is required to produce the magnetic anomaly high over the Vance axial valley. This magnetic modeling demonstrates that variations in the base of the magnetic source layer, which is assumed to be equivalent to the base of the extrusive lavas, can produce a significant proportion of the observed short-wavelength magnetic anomaly signal. These magnetic layer thickness models also correlate quite well with nearby seismic results which show that seismic layer 2A thins beneath the axial valley of the Cleft and is thicker beneath the Vance axial valley. Recent seismic results over other fast and medium spreading rifts also show rapid changes in the thickness of the uppermost crust near the axis of spreading, which could produce significant magnetic contrasts. The results of this study and the correlation with independent seismic measurements suggest that while magnetization may vary due to geomagnetic behavior or because of petrology or alteration, first-order change in upper crustal thickness is one of the most important variables to consider in the production of fine-scale magnetic anomalies in young ocean crust.