We report the field observation of hydrate deposits of different crystal structures in the same cores of a mud volcano in the Kukuy Canyon. We link those deposits to chemical fractionation during gas hydrate crystallization. Gas composition and crystallographic analyses of hydrate samples reveal involvement of two distinct gas source types in gas hydrate formation at present or in the past: microbial (methane) and thermogenic (methane and ethane) gas types. The clathrate structure II, observed for the first time in fresh water sediments, is believed to be formed by higher mixing of thermogenic gas.