Many examples of local magnetic anomalies in the vicinity of active faults have been reported, although the association of magnetic anomalies with active faults has not been well established. Aiming at studying local magnetic anomalies, we made magnetic surveys in Beppu Bay, Southwest Japan, where many active faults have been found through acoustic sounding. Along individual survey profiles, we found many magnetic anomalies seemingly associated with active faults, but in the contour maps of the geomagnetic total intensity and the shaded relief maps, no clear lineation-like feature could be identified. Profile data could be interpreted in terms of either a model of spatial magnetization variation or a model of magnetic basement undulation. The former model implies the correspondence of a low magnetization zone to a fractured zone, whereas the latter model suggests the depression of magnetic basement.