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Abstract Molecular and stable isotope compositions of hydrate-bound gases collected from 59 hydrate-bearing sites between 2005 to 2019 in the southern and central sub-basins of Lake Baikal are reported. The δ2H of the hydrate-bound methane is distributed between − 310‰ and − 270‰, approximately 120‰ lower than its value in the marine environment, due to the difference in δ2H between the lake water and seawater. Hydrate-bound gases originate from microbial (primary and secondary), thermogenic, and mixed gas sources. Gas hydrates with microbial ethane (δ13C: − 60‰, δ2H: between − 310‰ and − 250‰) were retrieved at approximately one-third of the total sites, and their stable isotope compositions were lower than those of thermogenic ethane (δ13C: − 25‰, δ2H: − 210‰). The low δ2H of ethane, which has rarely been reported, suggests for the first time that lake water with low hydrogen isotope ratios affects the formation process of microbial ethane as well as methane. Structure II hydrates containing enclathrated methane and ethane were collected from eight sites. In thermogenic gas, hydrocarbons heavier than ethane are biodegraded, resulting in a unique system of mixed methane-ethane gases. The decomposition and recrystallization of the hydrates that enclathrate methane and ethane resulted in the formation of structure II hydrates due to the enrichment of ethane.