Carbon (C) densities of the tree biomass and soil (0–50 cm) in indigenous forest and plantations of eucalyptus, cypress and pine in the Taita Hills, Kenya were determined and compared. The cypress and pine plantations were about 30-years-old and eucalyptus plantations about 50-years-old. Biomass C densities were estimated from breast height diameter and wood density using allometric functions developed for tropical species and an assumed C content of 50%. Belowground biomass C densities were estimated using root:shoot biomass ratios. Soil organic C (SOC) densities were calculated from measured organic carbon contents (0–20 and 20–50 cm layers) and modelled bulk density values. Mean total biomass C and SOC densities for indigenous forest were greater than those of the plantations, and the difference was significant (p < 0.05) in the cases of cypress and pine biomass and pine SOC. The correlation between biomass C and SOC densities was nearly significant in the case of indigenous forest, but negative. Biomass C densities were not significantly correlated with mean annual precipitation, mean annual temperature or potential evapotranspiration, but pine biomass C densities were significantly correlated to actual evapotranspiration. SOC densities were more strongly correlated to mean annual precipitation than biomass C densities, but only significantly so in the case of pine. Neither biomass C nor SOC densities were correlated to plant available water capacity of the soil. Indigenous forest SOC densities were significantly correlated to soil clay contents, but negatively. Indigenous forests sequester more C in biomass and soil than do 30 to 50-year-old plantations of exotics, but it remains unclear if this is an intrinsic difference between indigenous forest and plantations of exotics or because of insufficient time for SOC levels in plantations to recover after clearance of original indigenous forest.