Abstract The molecular and stable isotope compositions of coalbed gases from the Upper Carboniferous strata and natural gases accumulated within the autochthonous Upper Miocene Skawina Formation of the Dębowiec-Simoradz gas deposit were determined, as well as the chemical and stable isotope compositions of waters from the Skawina Formation and waters at the top of the Upper Carboniferous strata of the Kaczyce Ridge (the abandoned “Morcinek” coal mine) in the South-Western part of the Upper Silesian Coal Basin. Two genetic types of natural gases within the Upper Carboniferous coal-bearing strata were identified: thermogenic (CH 4, small amounts of higher gaseous hydrocarbons, and CO 2) and microbial (CH 4, very small amounts of ethane, and CO 2). Thermogenic gases were generated during the bituminous stage of coalification and completed at the end of the Variscan orogeny. Degassing (desorption) of thermogenic gases began at the end of late Carboniferous until the late Miocene time-period and extended to the present-day. This process took place in the Upper Carboniferous strata up to a depth of about 550 m under the sealing Upper Miocene cover. A primary accumulation zone of indigenous, thermogenic gases is present below the degassing zone. Up to 200 m depth from the top of the Upper Carboniferous strata, within the weathered complex, an accumulation zone of secondary, microbial gas occurs. Waters within these strata are mainly of meteoric origin of the infiltration period just before the last sea transgression in the late Miocene and partly of marine origin having migrated from the Upper Miocene strata. Then, both methanogenic archaebacteria and their nutrients were transported by meteoric water into the near-surface Carboniferous strata where the generated microbial CH 4 saturated coal seams. Waters within the Miocene strata of the Dębowiec-Simoradz and Zabłocie are of marine origin, and natural gases accumulated within autochthonous Miocene strata of the Dębowiec-Simoradz gas deposit were most probably generated by microbial processes of on organic matter dispersed within the strata, though some contribution of gases migrating from the Carboniferous coal-bearing strata cannot be excluded.