We reported the characteristics of hydrate-bound hydrocarbons in lake-bottom sediments at the Kedr mud volcano in Lake Baikal. Twenty hydrate-bearing sediment cores were retrieved, and methane-stable isotopes of hydrate-bound gases (δ¹³C and δ²H of − 47.8‰ to − 44.0‰ V-PDB and − 280.5‰ to − 272.8‰ V-SMOW, respectively) indicated their thermogenic origin accompanied with secondary microbial methane. Powder X-ray diffraction patterns of the crystals and molecular composition of the hydrate-bound gases suggested that structure II crystals showed a high concentration of ethane (around 14% of hydrate-bound hydrocarbons), whereas structure I crystals showed a relatively low concentration of ethane (2–5% of hydrate-bound hydrocarbons). These different crystallographic structures comprised complicated layers in the sub-lacustrine sediment, suggesting that the gas hydrates partly dissociate, concentrate ethane and form structure II crystals. We concluded that a high concentration of thermogenic ethane primarily controls the crystallographic structure of gas hydrates and that propane, iso-butane (2-methylpropane) and neopentane (2,2-dimethylpropane) are encaged into crystals in the re-crystallisation process.