The formation of authigenic pyrite in marine sediments involves multiple reactions between ferrous iron (Fe2+) and hydrogen sulfide (H2S). Ferrous iron is commonly provided through the reductive dissolution of Fe-(oxyhydr)oxides by organic matter (i.e., dissimilatory Fe reduction), dissolved sulfide (i.e., abiotic Fe reduction) or methane (i.e., Fe-AOM), whereas sulfide is supplied by organoclastic sulfate reduction (OSR) or sulfate-driven anaerobic oxidation of methane (SD-AOM). Since Rayleigh-type distillation operates widely in sediments of gas-hydrate-bearing zones, sulfur and nickel isotope compositions (i.e., δ34S and δ60Ni) cannot readily distinguish OSR- from SD-AOM-associated pyrite. However, these microbial pathways may yield different patterns of trace-element enrichment in pyrite. To better understand the linkage of trace-element patterns to specific microbial pathways (i.e., Fe reduction, Fe-AOM, OSR and SD-AOM), and to evaluate the use of S and Ni isotopic signatures as tracers for pyrite formation pathways in methane-rich sediments, we report pyrite-associated trace element and δ34S and δ60Ni isotope analyses of sediments from a gas hydrate borehole (Site GMGS4-SC-03) from the Shenhu area, Pearl River Mouth Basin, South China Sea. Pyrite formed in conjunction with Fe- and/or SD-AOM exhibits abundant framboidal overgrowths and extremely high δ34S (up to +142.8‰) and δ60Ni (up to +2.72‰), representing the highest stable S and Ni isotopic compositions of pyrite reported to date. These pyrite morphologies are enriched in Co and Ni, which may be a diagnostic signature of an SD-AOM pathway. By contrast, OSR-associated pyrite is enriched in Cu and Zn due to OSR-induced release of trace elements from decaying organic matter. In addition, the relationship of As to Cu and/or Zn can distinguish microbial Fe/Mn reduction from Fe/Mn-AOM, because microbial Fe/Mn reduction releases trace elements from both Fe/Mn-(oxyhydr)oxides (i.e., As) and organic matter (i.e., Cu and Zn), whereas Fe/Mn-AOM only releases trace elements from Fe/Mn-(oxyhydr)oxides. Furthermore, an observed covariation between As and either Co or Ni in most pyrite with high δ34S, indicates that this pyrite captured both As released during Fe/Mn-AOM and Co and Ni from SD-AOM. Thus, the high nickel isotope values measured in this study likely dominantly reflect release of isotopically heavy Ni from Fe- and Mn-(oxyhydr)oxides. Our results demonstrate that the trace-element composition of pyrite in gas-hydrate-bearing sediments can record the geochemical signature of the dominant microbial processes.