Running along the middle of the Philippine archipelago from south to north, the Philippine fault zone is one of the world’s major strike-slip faults. Intense volcanism in the archipelago is attributed to the ongoing subduction along the trench systems surrounding it. This study interprets the magnetic data covering the Philippine fault zone and the bounding archipelago subduction systems to understand the structural characteristics of the study area. Magnetic data analysis suggests that the Philippine fault is roughly distributed along the boundary of high/low magnetization and separates the different amplitude features of the first order analytic signal. Visayas province is a specific area bounded by the other parts of the Philippine archipelago. Further differentiating the tectonic units, the proto-Southeast Bohol Trench should be the main tectonic boundary between Visayas and Mindanao. A clear NE - SW boundary separates Luzon from Visayas as shown by the variant depths to the top of the magnetic basement. This boundary could suggest the different tectonic characteristics of the two regions.