Conodont colour alteration indices (CAI) have been used to recognize the thermal maturation of the Middle Devonian to Late Carboniferous sedimentary infill of the Ahnet and Mouydir basins in southern Algeria. The study is based on a large set of conodont samples obtained from 69 sections and outcrops. In the Ahnet Basin, the Middle and Upper Devonian rocks at the surface show a uniform thermal maturity level characterized by the CAI values of 2, which suggests maximum burial temperatures about 50 °C. In contrast, the Carboniferous exposures yield a wide range of CAI values from 1 to 3.5. Besides, the general tendency in maturity decreases upward in the sequence, there are anomalies related to heating by small local magmatic bodies. In the Mouydir Basin, the CAI values in the Middle and Upper Devonian outcrops range from 2 to 3.5. The pattern indicates that the majority of Middle Devonian rocks have experienced burial temperatures of about 120 °C, while thermal maturation of the Upper Devonian strata is clearly lower, with maximum heating temperatures about 50 °C at the edges of the basin. The observed thermal maturity has been mostly achieved during Late Carboniferous time, prior to the Variscan inversion, and only locally during the Mesozoic. It is a product of loading by Carboniferous overburden succession of which part is now removed, approx. 200–1300 m in the Ahnet Basin and up to 1200 m in the Mouydir Basin. The analysis of palaeotemperatures suggests an average geothermal gradient of 30 °C/km during Carboniferous time in the Ahnet–Mouydir area. In terms of hydrocarbon exploration the studied Devonian succession is predominantly mature for oil and gas. In contrary, the Carboniferous rocks are immature. Higher maturities are likely to occur in the subsurface.