Measurements of ecosystem carbon (C) fluxes in temperate forests are concentrated in the Northern Hemisphere, leaving the functionally diverse temperate forests in the Southern Hemisphere underrepresented. Here, we report three years (February 2018-January 2021) of C fluxes, studied with eddy-covariance and closed chamber techniques, in an endangered temperate evergreen rainforest of the long-lived paleoendemic South American conifer Fitzroya cupressoides. Using classification and regression trees we analyzed the most relevant drivers and thresholds of daily net ecosystem exchange (NEE) and soil respiration. The annual NEE showed that the forest was a moderate C sink during the period analyzed (-287±38 g C m-2 year -1). We found that the capacity to capture C of the Fitzroya rainforests in the Coastal Range of southern Chile is optimal under cool and rainy conditions in the early austral spring (October-November) and decreases rapidly towards the summer dry season (January-February) and autumn. Although the studied forest type has a narrow geographical coverage, the gross primary productivity measured at the tower was highly representative of Fitzroya and other rainforests in the region. Our results suggest that C fluxes in paleoendemic cool F. cupressoides forests may be negatively affected by the warming and drying predicted by climate change models, reinforcing the importance of maintaining this and other long-term ecological research sites in the Southern Hemisphere.