Extremely negative carbon isotope values from the Doushantuo cap dolostone succession in the Yangtze Gorges, South China were interpreted as direct evidence of the hypothesis of methane hydrate destabilization during the Marinoan deglaciation. However, this suggestion remains uncertain due to the obscurity of the paragenetic sequence of carbonate minerals with diverse carbon isotopic compositions. Here, we conducted macroscopic and microscopic petrographic and carbon isotopic investigations of the cap dolostone succession at the Jiulongwan section in the Yangtze Gorges. Our results show that extreme δ 13C values down to − 44‰ exclusively occur in calcite, whereas δ 13C values for the host dolomite range mostly between − 4‰ and − 2‰, and clearly reveal that the host dolomite were locally dissolved and/or replaced by the calcite bearing highly 13C-depleted signals. This finding suggests that methane-oxidation activity as indicated by the strongly depleted δ 13C signals did not occur until after the cap dolostone deposition. Thus, the presence of the extremely negative δ 13C values could not be taken as evidence for the proposed methane hypothesis. Nevertheless, this conclusion is not contradictory to the scenario that massive releases of methane from permafrost hydrates during deglaciation, much prior to methane oxidation documented here, could drive substantial negative δ 13C shifts well exhibited by the Doushantuo cap dolostone and others around the world.