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 methane over ethane plus propane (C1/C2+3) have traditionally been applied to infer methane sources, 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 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 (oil seeps, pockmarks, mud volcanoes, and other cold seeps). The average apparent equilibration temperatures of methane from the Δ13CH3D (the excess abundance of 13CH3D relative to the stochastic distribution) geothermometer 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 methane 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 mud volcanoes 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 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 on km-thick sediments in tectonically less active or passive settings (Black Sea, North Atlantic) 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.