Abstract During studies of unconventional natural gas reservoirs of Silurian and Ordovician age in the northern Appalachian basin we observed complete reversal of the normal trend of carbon isotopic composition, such that δ 13 C methane (C 1 ) >δ 13 C ethane (C 2 ) >δ 13 C propane (C 3 ). In addition, we have observed isotopic reversals in the δ 2 H in the deepest samples. Isotopic reversals cannot be explained by current models of hydrocarbon gas generation. Previous observations of partial isotopic reversals have been explained by mixing between gases from different sources and thermal maturities. We have constructed a model which, in addition to mixing, requires Rayleigh fractionation of C 2 and C 3 to cause enrichment in 13 C and create reversals. In the deepest samples, the normal trend of increasing enrichment of 13 C and 2 H in methane with increasing depth reverses and 2 H becomes depleted as 13 C becomes enriched. We propose that the reactions that drive Rayleigh fractionation of C 2 and C 3 involve redox reactions with transition metals and water at late stages of catagenesis at temperatures on the order of 250–300 °C. Published ab initio calculated fractionation factors for C–C bond breaking in ethane at these temperatures are consistent with our observations. The reversed trend in δ 2 H in methane appears to be caused by isotopic exchange with formation water at the same temperatures. Our interpretation that Rayleigh fractionation during redox reactions is causing isotopic reversals has important implications for natural gas resources in deeply buried sedimentary basins.