Gas hydrates stored in the continental margins of the world’s oceans represent the largest global reservoirs of methane. Determining the source and history of methane from gas hydrate deposits informs the viability of sites as energy resources, and potential hazards from hydrate dissociation or intense methane degassing from ocean warming. Stable isotope ratios of methane (13C/12C, D/H) and the molecular ratio of light hydrocarbons (C1/C2+3) have traditionally been applied to infer methane source, but often yield ambiguous results when two or more sources are mixed, or when compositions were altered by physical (e.g., diffusion) or microbial (e.g., methanotrophy) processes. We measured the abundance of clumped methane isotopologue (13CH3D) alongside 13C/12C and D/H of methane, and C1/C2+3 (the ratio of methane over ethane plus propane) for 46 submarine gas hydrate specimens and associated vent gases from 11 regions of the world’s oceans. These samples are associated with different seafloor seepage features (cold seeps, oil seeps, pockmarks, and mud volcanoes). The values of Δ13CH3D (the excess abundance of 13CH3D relative to the stochastic distribution) and apparent equilibration temperatures increase from cold seeps (15 to 65 ℃) and pockmarks (36 to 54 ℃), to oil-associated gas hydrates (48 to 120 ℃). These apparent temperatures are consistent with, or a few tens of degrees higher than, the temperature expected for putative microbial sources. Apparent methane generation depths were derived for cold seep, pockmark, and oil seep methane from isotopologue-based temperatures and the local geothermal gradients. Estimated methane generation depths ranged from 0.2 to 5.3 kmbsf, and are largely consistent with source rock information, and other chemical geothermometers based on clay mineralogy and fluid chemistry (e.g., Cl, B, and Li). Methane associated with mud volcanoes yielded a wide range of apparent temperatures (15 to 313℃). Gas hydrates from the Kumano Basin and Mediterranean Sea yielded δ13C-CH4 values from -36.9 to -51.0‰, typical for thermogenic sources. Δ13CH3D values (3.8 to 6.0‰) from these sites, however, are consistent with prevailing microbial sources. These mud volcanoes (Kumano Basin, Mediterranean Sea) are located at active convergent plate margins, where hydrogen may be supplied from basement rocks, and fuel methanogenesis to the point of substrate depletion. In contrast, gas hydrate from mud volcanoes located in tectonically passive settings (Sorokin Trough, Black Sea; Håkon Mosby Mud Volcano, Barents Sea slope) yielded microbial-like δ13C-CH4 and C1/C2+3 values, and low Δ13CH3D values (1.6 to 3.3‰), which may be due to kinetic isotope effects. This study is the first to document the link between methane isotopologue-based temperature estimates and key submarine gas hydrate seepage features, and validate previous models about their geologic driving forces.