Abstract Methane and CO 2 emissions from the two most active mud volcanoes in central Japan, Murono and Kamou (Tokamachi City, Niigata Basin), were measured in from both craters or vents (macro-seepage) and invisible exhalation from the soil (mini- and microseepage). Molecular and isotopic compositions of the released gases were also determined. Gas is thermogenic ( δ 13C CH4 from −32.9‰ to −36.2‰), likely associated with oil, and enrichments of 13C in CO 2 ( δ 13C CO2 up to +28.3‰) and propane ( δ 13C C3H8 up to −8.6‰) suggest subsurface petroleum biodegradation. Gas source and post-genetic alteration processes did not change from 2004 to 2010. Methane flux ranged within the orders of magnitude of 10 1–10 4 g m −2 d −1 in macro-seeps, and up to 446 g m −2 d −1 from diffuse seepage. Positive CH 4 fluxes from dry soil were widespread throughout the investigated areas. Total CH 4 emission from Murono and Kamou were estimated to be at least 20 and 3.7 ton a −1, respectively, of which more than half was from invisible seepage surrounding the mud volcano vents. At the macro-seeps, CO 2 fluxes were directly proportional to CH 4 fluxes, and the volumetric ratios between CH 4 flux and CO 2 flux were similar to the compositional CH 4/CO 2 volume ratio. Macro-seep flux data, in addition to those of other 13 mud volcanoes, supported the hypothesis that molecular fractionation (increase of the “Bernard ratio” C 1/(C 2 + C 3)) is inversely proportional to gas migration fluxes. The CH 4 “emission factor” (total measured output divided by investigated seepage area) was similar to that derived in other mud volcanoes of the same size and activity. The updated global “emission-factor” data-set, now including 27 mud volcanoes from different countries, suggests that previous estimates of global CH 4 emission from mud volcanoes may be significantly underestimated.