In this paper, we present the results of down core variations in magnetic susceptibility and magnetic mineral composition of fifteen piston cores retrieved from the active continental margin offshore of southwestern Taiwan, where a wide distribution of bottom simulating reflectors (BSRs) related to gas hydrate layers has been detected. X-ray analysis on magnetic extracts from the cores indicates that detrital magnetite and authigenic greigite, in various proportions, are the dominant magnetic minerals in sediments. Non-magnetic, authigenic pyrite is generally associated with greigite, but it may co-exist with magnetite or may solely occur in sediments. Consequently, the sediment sequences of the fifteen piston cores have complicated magnetic mineral assemblages that result in various magnetic susceptibility profiles. For core segments containing detrital magnetite as the only magnetic mineral, values of magnetic susceptibility are moderate with small variations (8 - 15 × 10-6 SI), which can be regarded as the susceptibility backgrounds for the initially deposited sediments. However, high magnetic susceptibilities relative to the backgrounds were found in core segments where magnetic mineral is enriched in greigite. Magnetic susceptibilities lower than the backgrounds were found in segments where neither magnetite nor greigite were detected. The complicated occurrence of magnetic minerals reveals that their host sediments at different levels have suffered various degrees of early diagenetic process ranging from oxic to anoxic conditions. Due to very low sedimentary organic matter content in the study area, detrital magnetite persisted in sediments that were subjected to initially oxic (or sub-oxic) conditions. However, the sedimentary organic matter is apparently insufficient for providing reducing environments for the formation or enrichment of authigenic iron sulfides. Instead, we propose that gaseous methane derived from gas hydrates in deeper sedimentary layers should be the most likely source of extra organic matter. The different flux intensities of this gas either through slow diffusion or rapid venting resulted in various anoxic conditions, which caused the dissolution or survival of magnetite and the formation or enrichment of greigite and pyrite.