Methane emissions from the subsurface are common in the Karoo. There have been frequent anecdotal reports of explosive gas in boreholes, both dry and wet in the Karoo. In some cases the gas is identified as methane. Thermal spring water in the Karoo invariably contains some amounts of methane and pockets have been found during tunnelling projects and in some deep Soekor boreholes. Some groundwater in the region of the Gariep Dam indicated substantial quantities of methane and an association with helium and hydrogen sulphide. The isotope concentrations of carbon and hydrogen in methane characterise the methane formation processes. Isotope values for samples from the central Karoo basin are consistent with those of thermogenic gas found elsewhere in the world. Towards the northern and eastern fringes of the basin, lower δ13C values suggest that the preponderance of methane is produced by microbial processes. The presence of thermogenic methane together with helium on the surface is likely to give clues to pathways from depth. Exploration for shale gas in the deep Ecca will need to include isotope analysis for any contemplated baseline study.