Despite the importance of Arctic and boreal regions in the present carbon cycle, estimates of annual high-latitude carbon fluxes vary in sign and magnitude. Without accurate estimates of current carbon fluxes from Arctic and boreal ecosystems, predicting the response of these systems to global change is daunting. A number of factors control carbon turnover in high-latitude soils, but because they are unique to northern systems, they are mostly ignored by biogeochemical models used to predict the response of these systems to global change. Here, we review those factors. First, many northern systems are dominated by mosses, whose extremely slow decomposition is not predicted by commonly used indices of litter quality. Second, cold temperature, permafrost, waterlogging, and substrate quality interact to stabilize soil organic matter, but the relative importance of these factors, and how they respond to climate change, is unknown. Third, recent evidence suggests that biological activity occurring over winter can contribute significantly to annual soil carbon fluxes. However, the controls over this winter activity remain poorly understood. Finally, processes at the landscape scale, such as fire, permafrost dynamics, and drainage, control regional carbon fluxes, complicating the extrapolation of site-level measurements to regional scales.