An extensive subsurface investigation evaluating the geothermal energy resources and underground thermal energy storage potential is being carried out in the southwestern part of the Swiss Molasse Basin around the Geneva Canton. Among this process, the evaluation of the petroleum source-rock type and potential is an important step to understand the petroleum system responsible of some oil and gas shows at surface and subsurface. This study provides a first appraisal of the risk to encounter possible undesired occurrence of hydrocarbons in the subsurface of the Geneva Basin. Upon the numerous source-rocks mentioned in the petroleum systems of the North Alpine Foreland Basin, the marine Type II Toarcian shales (Lias) and the terrigenous Type III Carboniferous coals and shales have been sampled from wells and characterized with Rock–Eval pyrolysis and GC–MS analysis. The Toarcian shales (known as the Posidonia shales) are showing a dominant Type II organic matter composition with a Type III component in the Jura region and the south of the basin. Its thermal maturity (~ 0.7 VRr%) shows that this source-rock currently generates hydrocarbons at depth. The Carboniferous coals and shales show a dominant Type III organic matter with slight marine to lacustrine component, in the wet gas window below the Geneva Basin. Two bitumen samples retrieved at surface (Roulave stream) and in a shallow borehole (Satigny) are heavily biodegraded. Relative abundance of regular steranes of the Roulave bitumen indicates an origin from a marine Type II organic matter. The source of the Satigny bitumen is supposedly the same even though a deeper source-rock, such as the lacustrine Permian shales expelling oil in the Jura region, can’t be discarded. The oil-prone Toarcian shales in the oil window are the most likely source of this bitumen. A gas pocket encountered in the shallow well of Satigny (Geneva Canton), was investigated for molecular and stable isotopic gas composition. The analyses indicated that the gas is made of a mixture of microbial (very low δ13C1) and thermogenic gas. The isotopic composition of ethane and propane suggests a thermogenic origin from an overmature Type II source-rock (> 1.6 VRr%) or from a terrigenous Type III source at a maturity of ~ 1.2 VRr%. The Carboniferous seems to be the only source-rock satisfying these constraints at depth. The petroleum potential of the marine Toarcian shales below the Geneva Basin remains nevertheless limited given the limited thickness of the source-rock across the area and does not pose a high risk for geothermal exploration. A higher risk is assigned to Permian and Carboniferous source-rocks at depth where they reached gas window maturity and generated large amount of gas below sealing Triassic evaporites. The large amount of faults and fractures cross-cutting the entire stratigraphic succession in the basin certainly serve as preferential migration pathways for gas, explaining its presence in shallow stratigraphic levels such as at Satigny.