The importance of the magnetic iron sulfide minerals, greigite (Fe3S4) and pyrrhotite (Fe7S8), is often underappreciated in geochemical studies because they are metastable with respect to pyrite (FeS2). Based on magnetic properties and X-ray diffraction analysis, previous studies have reported widespread occurrences of these magnetic minerals along with magnetite (Fe3O4) in two thick Plio-Pleistocene marine sedimentary sequences from southwestern Taiwan. Different stratigraphic zones were classified according to the dominant magnetic mineral assemblages (greigite-, pyrrhotite-, and magnetite-dominated zones). Greigite and pyrrhotite are intimately associated with fine-grained sediments, whereas magnetite is more abundant in coarse-grained sediments. We measured total organic carbon (TOC), total sulfur (TS), total iron (FeT), 1N HCl extractable iron (FeA), and bulk sediment grain size for different stratigraphic zones in order to understand the factors governing the formation and preservation of the two magnetic iron sulfide minerals. The studied sediments have low TS/FeA weight ratios (0.03–0.2), far below that of pyrite (1.15), which indicates that an excess of reactive iron was available for pyritization. Observed low TS (0.05–0.27%) is attributed to the low organic carbon contents (TOC=0.25–0.55%), which resulted from dilution by rapid terrigenous sedimentation. The fine-grained sediments also have the highest FeT and FeA values. We suggest that under conditions of low organic carbon provision, the high iron activity in the fine-grained sediments may have removed reduced sulfur so effectively that pyritization was arrested or retarded, which, in turn, favored preservation of the intermediate magnetic iron sulfides. The relative abundances of reactive iron and labile organic carbon appear to have controlled the transformation pathway of amorphous FeS into greigite or into pyrrhotite. Compared to pyrrhotite-dominated sediments, greigite-dominated sediments are finer-grained and have higher FeA but lower TS. We suggest that diagenetic environments with higher supply of reactive iron, lower supply of labile organic matter, and, consequently, lower sulfide concentration result in relatively high Eh conditions, which favor formation of greigite relative to pyrrhotite.