Abstract In several recent published studies, paleomagnetic results from greigite-bearing sediments reveal characteristic remanences that are anti-parallel to those carried by coexisting detrital magnetic minerals and polarities that are opposite to those expected for the age of the rock unit. These observations have important implications for the reliability of paleomagnetic data from greigite-bearing sediments. We have investigated the origin of such contradictory magnetic polarities by studying the formation mechanisms of greigite in mudstones from the Lower Gutingkeng Formation, southwestern Taiwan. Scanning electron microscope observations indicate that the Gutingkeng greigite has three modes of occurrence, including nodular, framboidal and matrix greigite. Microtextural observations, including transection of bedding by iron-sulfide nodules with no deviation of sediment textures, the presence of partially dissolved edges around detrital and early diagenetic phases, and neoformation of greigite and Fe-rich clays around detrital phyllosilicates, indicate that all three types of greigite have a diagenetic origin that post-dates early diagenetic pyrite. In addition, paleomagnetic data yield contradictory polarities even for greigite-bearing sister samples from the same stratigraphic horizon. The data are collectively interpreted to indicate that neoformation of the Gutingkeng greigite occurred after partial dissolution of syngenetic or early diagenetic pyrite. The timing of greigite formation can apparently vary enough to give contradictory polarities for different greigite components even within a single stratigraphic horizon. Direct petrographic observation of authigenic magnetic iron-sulfide phases, as carried out in this study, can provide important constraints on formation mechanisms and timing of remanence acquisition for these minerals and suggests that care should be taken when interpreting magnetostratigraphic data from greigite-bearing sediments.