Authigenic carbonates of the northern Okinawa Trough have been shown to be contributed by both sulfate- and Fe-driven anaerobic oxidation of methane (SD-AOM and Fe-AOM, respectively); however, the microorganisms involved remain poorly constrained. To better understand the types and roles of microorganisms in specific biological methane oxidation processes, authigenic carbonates collected from the northern Okinawa Trough at water depths between ~540 m and 700 m were studied using petrographic, mineralogical, elemental, and lipid biomarker analyses. The carbonate minerals were primarily aragonite, high-magnesium calcite, low-magnesium calcite, or dolomite. The extremely low δ13C values of bulk carbonates (–59.2‰), molecular fossils of anaerobic methane oxidizing archaea (ANME; –131‰), and sulfate-reducing bacteria (SRB; –77‰) indicated that the authigenic carbonates formed as products of AOM. Biogenic methane was confirmed to be the main carbon source for all carbonates, whereas bio-degraded oil and hydrothermal input complemented carbon sources, as revealed by the occurrence of unresolved complex mixture, strongly enriched As and Sb, and their correlations with Fe/Al. Combined with enriched δ18O values (as high as +5‰), the methane fluids were suggested to derive from the dissociation of gas hydrates. ANME-2 and a mixture of ANME-1 and ANME-2 were identified for the two calcitic carbonates, respectively, as revealed by their specific biomarker patterns. The relatively higher contents of 13C-depeleted isoprenoids and SRB–related fatty acids, strong Mo enrichment, and biological debris in both calcite- and aragonite-dominated carbonates reflect precipitation driven by SD-AOM in a shallow sulfate-methane transition. For other seep carbonates, low amounts of 13C-depeleted isoprenoids and the near absence of crocetane suggest dominance of the ANME-1 assemblage. The extremely low amounts and non-13C-depleted iso-/anteiso-C15:0 fatty acids (–27‰) in the dolomite-containing carbonates indicate the decoupling of ANME and SRB. These carbonates were most likely formed below or at the bottom of the sulfate-methane transition and included contributions from Fe-AOM, as indicated by the low Mo content, occurrence of dolomite and siderite, and decreased δ56Fe values with increasing Fe/Al ratios.