Four massive brecciated, chimney-like, and slender pipe network carbonate samples (JA-4, JA-5, JX-8 and BG-12) were collected from southwestern Taiwan, which were suggested to have formed as a result of anaerobic oxidization of methane (AOM). Considering that the environmental conditions of the carbonates precipitation and the sources of carbon and organic matter need to be further declared, molecular fossils and compound-specific carbon isotopic investigations of the carbonates were conducted in this study. According to lipid biomarkers of 2,6,10,15,19-pentamethyleicosane (PMI) and squalane diagnostic to methanotrophic archaea, as well as the extremely low δ13C values (as low as ?113.4‰) detected in samples JA-4, JA-5 and JX-8, these carbonates were revealed to be a result of AOM. Based on the varied δ13C values of characteristic archaea biomarkers in specific samples, biogenic methane was proposed to be responsible for the formation of samples JA-4 and JA-5, whereas a mixed carbon source of 13C-depleted methane and 13C-enriched residual CO2 from methanogenesis was suggested for the carbonate of JX-8 due to the co-occurrence of a highly positive δ13Ccarb value (+8‰) and a moderate 13C depletion of PMI. The low content of AOM-related biomarkers and the absence of indicators for ANME-2 suggested that these carbonates were formed in weak seep settings. By comparison, no typical lipid biomarkers for methanotrophic archaea was detected in carbonate BG-12. The short-chain and long-chain n-alkanes accounted for 30% and 45% of all hydrocarbons, respectively, with a CPI value of 1.2, suggesting that the n-alkanes were derived from both marine organisms and terrestrial inputs. A low thermal maturity could be revealed by the incomplete equilibrium value of the C31αβ 22S/(22S+22R) ratio (0.5), and the carbonate BG-12 was probably deposited in a suboxic condition indicated by a value of Pr/Ph ratio (2.5).