Natural gas is a key energy resource, and understanding how it forms is important for predicting where it forms in economically important volumes. However, the origin of dry thermogenic natural gas is one of the most controversial topics in petroleum geochemistry, with several differing hypotheses proposed, including kinetic processes (such as thermal cleavage, phase partitioning during migration, and demethylation of aromatic rings) and equilibrium processes (such as transition metal catalysis). The dominant paradigm is that it is a product of kinetically controlled cracking of long-chain hydrocarbons. Here we show that C2+n-alkane gases (ethane, propane, butane, and pentane) are initially produced by irreversible cracking chemistry, but, as thermal maturity increases, the isotopic distribution of these species approaches thermodynamic equilibrium, either at the conditions of gas formation or during reservoir storage, becoming indistinguishable from equilibrium in the most thermally mature gases. We also find that the pair of CO2 and C1 (methane) exhibit a separate pattern of mutual isotopic equilibrium (generally at reservoir conditions), suggesting that they form a second, quasi-equilibrated population, separate from the C2 to C5 compounds. This conclusion implies that new approaches should be taken to predicting the compositions of natural gases as functions of time, temperature, and source substrate. Additionally, an isotopically equilibrated state can serve as a reference frame for recognizing many secondary processes that may modify natural gases after their formation, such as biodegradation.