Carbon (C) sequestrated in the boreal forest ecosystems plays an important role in climate regulation. This study’s objectives were to quantify the differences in the components of the forest C cycle along a 1000 km latitudinal gradient within the boreal region and between dominant coniferous species in Fennoscandia. The study included seven xeric–sub-xeric and eight mesic–herb-rich heath forests dominated by Scots pine and Norway spruce, respectively. The total site carbon stock (CS) ranged from 81 to 260 Mg ha−1. The largest ecosystem component CSs were tree stems, mineral soil, and humus layer, representing 30 ± 2%, 28 ± 2%, and 13 ± 1% of total CS, respectively. On average, the spruce sites had 40% more C than the pine sites, and CS stored in most compartments was higher on spruce than on pine sites. As exceptions, understorey vegetation and litter layer had a larger CS on pine than on spruce sites. The northern sites had an average of 58% less C than the southern sites. Humus layer CS was the only compartment showing no latitudinal trends. Northern sites had a significantly larger fine and small root CS and understorey CS than southern sites. Most CS compartments were significantly correlated with litterfall C transfer components. Dissolved organic carbon (DOC) flux in throughfall was positively correlated with the aboveground tree compartment CS. Our study revealed patterns of C distribution in major boreal forest ecosystems along latitudinal and fertility gradients, which may serve as a reference for Earth system models and in the evaluation of their projections.