<p>Soil respiration is an important carbon flux and key process determining the net ecosystem production of terrestrial ecosystems. To address the enormous lack of quantification and understanding of seasonality in soil respiration of tropical forests in the Congo Basin, soil CO<sub>2</sub> fluxes and potential controlling factors were measured for the first time annually in two dominant forest types (lowland and montane) of the Congo Basin during three years at varying temporal resolution. Soil CO<sub>2</sub> fluxes from the Congo Basin resulted in 3.69 ± 1.22 and 3.82 ± 1.15 µmol CO<sub>2</sub> m<sup>−2</sup> s<sup>−1</sup> for lowland and montane forests, respectively. Respiration in montane forest soils showed a clear seasonality with decreasing flux rates during the dry season. Montane forest soil CO<sub>2</sub> fluxes were positively correlated with soil moisture while CO<sub>2</sub> fluxes in the lowland forest were not. Paired ẟ<sup>13</sup>C values of soil organic carbon (SOC) and soil CO<sub>2</sub> indicated that SOC in lowland forests is more decomposed than in montane forests, suggesting that respiration is controlled by C availability rather than environmental factors. In general, C in montane forests was more enriched in <sup>13</sup>C throughout the whole cascade of carbon intake via photosynthesis, litterfall, SOC, and soil CO<sub>2</sub> compared to lowland forests, pointing to a more open system. Even though soil CO<sub>2</sub> fluxes are similarly high in lowland and montane forests of the Congo Basin, the drivers of them were different, i.e. soil moisture for montane forest and C availability for lowland forest.</p>