The measurement of methane clumped isotopologues ( and ) allows exploring isotope bond ordering within methane molecules, and may reveal equilibrium temperatures. Whether such temperature reflects the formation or re-equilibration temperature of the methane is not well understood, but would have critical implications for the use of methane clumped isotopologues as geo-thermometers. Here we investigate gas bubbles from vigorous emissions at cold seeps (n = 14) in the Sea of Marmara, Turkey. These cold seeps are sourced from deeper sedimentary reservoirs. Conventional geochemical tracers such as carbon and hydrogen bulk isotopic ratios (13C/12C and D/H) or n-alkane molecular ratios, suggest these gases reflect various degrees of mixing between thermogenic and microbial sources. Some samples would generally be considered purely microbial in origin (; ‰). We report measurements of and showing that a fraction of those gases are in internal thermodynamic equilibrium, with the abundances of the two mass-18 isotopologues indicating concordant temperatures of ∼90 °C and ∼130 °C. These concordant temperatures are recorded by gases of putative microbial and thermogenic origin; the temperatures of equilibration are irrespective of the formation mechanism of the gases. We conclude that the two high-temperatures recorded by and are best explained by non-enzymatic re-equilibration at two local subsurface temperatures. First principles suggest that unequal rates of exchange are possible. Disequilibrium signatures where the two isotopologues yield discordant apparent temperatures are exhibited by other samples. In those cases the data define a trend of variable at nearly constant . These signatures are enigmatic, and we investigate and reject multiple possible explanations including mixing, diffusion or Anaerobic Oxidation of Methane. Different rates of re-equilibration between the two rare isotopologues are implied, although lacks experimental foundation at present. In general, all of these data point towards re-equilibration of the mass-18 methane isotopologues as an important process.