Abstract Many small and medium-sized Paleogene pull-apart basins in southern China contain an abundance of biogenic gas shows. Such shallow gas with biogenic characteristics has been thoroughly investigated only in Baise Basin. Hence, the research results from Baise Basin could serve as a model for the origin and characteristics of shallow gases in similar basins and areas in Southern China. There are ten gas fields with a total of proven reserves of 20 billion cubic meters discovered in Baise Basin. Three gas fields are located on the western and southern flank of the basin, and they are gas caps to heavy oil pools from depths between 600 m and 850 m. These accumulations contain dry biogenic gases, with C1/C1-5 exceeding 0.99, light δ13C1 (–76 to −54‰), and heavy δD1 (−218‰). Trace heavy gaseous hydrocarbons are strongly biodegraded (iC4/nC4>3). The other seven gas fields are located in the northern fault zone and the central Nakun uplift of the basin at depths between 300 m and 700 m. Gases are mainly unassociated and condensed gases. The condensed gases are depleted in 13C (δ13C1: −67 to −53.7‰, δ13C2: −52.3 to −36.1‰, δ13C3: −43.3 to −33.4‰), but wet with C1/C2+3 mostly less than 20, suggesting a mainly thermal origin at low maturity. The unassociated gases are dominated by methane, with C1/C2+3 ratio above 100, variable N2 (0 to 5.4%), and traces of CO2. The δ13C value of methane in the unassociated gases is between −76 to −60‰, and δD1 values from −248 to −213.7‰. These gases also contain isotopically light ethane with δ13C2 values of −64.5 to −42‰, which we infer to have originated from deeper horizons as a result of migration or diffusion from low-maturity thermal gases with light stable carbon isotopic compositions (C1/C2+3 <20, δ13C2 from −60‰ to −58‰). A similar thermal origin is inferred for the other heavy gaseous hydrocarbons. Formation water with the shallow gases of this basin is mainly NaHCO3-type with low TDS ranging from 1000 to 4500 ppm. The (HCO3+CO3)/Cl ratios range from 1.5 to 100, indicating a relative open hydrodynamic condition and the possible intrusion of meteoric water. These data indicate that early biogenic gas generated syndepositionally was probably not preserved, and that the current biogenic gas accumulation formed mainly as a result post-depositional of crude oil biodegradation in the western basin and coal biodegradation in the northern fault zone. Shallow gases in Baise Basin are mainly secondary biogenic gases, with an admixture of low maturity thermogenic gases from deeper horizons.