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Gas hydrates are one of the largest pools of readily exchangeable carbon on Earth surface. Releases of the greenhouse gas methane from hydrates are responsible for a number of important climate changes in geological history. Many of the inferred events were based on the δ13C values of carbonates, which have been challenged lately. Here we propose a molecular fossil proxy “Methane Index (MI)” to better document the destabilization of marine gas hydrates. MI is constructed by the relative distribution of glycerol dialkyl glycerol tetraethers (GDGTs), the core membrane lipids of Archaea. Our study in the Gulf of Mexico sediments clearly shows the correlation between gas venting, microbial community and lipid profile shifts and the MI, corroborating the idea that MI might be a robust indicator for hydrate dissociation. MI provides us a more precise and effective proxy for evaluating the gas hydrate instability in Earth’s geological history.