In this paper, the origin, maturity, migration, biodegradation and mixing of natural hydrocarbon gases in Japan have been interpreted using molecular and carbon isotope compositions. No indications of abiogenic gases have been found, the gases being classified as microbial, thermogenic or mixed microbial/thermogenic. However, secondary alteration (mixing, biodegradation, fractionation in migration processes) has had a major but variable impact on the composition of natural gases. Biodegradation, especially, has altered both molecular and isotopic signatures. Thus, the prime control of isotopic and molecular characteristics in gases is due to genetic phenomena, but secondary effects must be taken into account when attempting to understand the origin and distribution of gas. Where the extent of secondary alteration is small, carbon isotope compositions of thermogenic hydrocarbons are controlled largely by maturity. An isotope model developed by Berner and Faber was applied successfully to natural gases in northeast Japan. Besides maturity estimation, the application of the model enables detection of biodegradation, mixing between microbial and thermogenic gases, and mixing among gases with different maturities. The carbon isotope compositions of carbon dioxide also provide information for their genetic origins.