Integrated studies based on the flux tower network during the past two decades reveal the spatial variability of the annual values of net ecosystem production (NEP) in different terrestrial ecosystems. These ecosystems act as a huge carbon sink for human-induced CO2 emissions as a whole. Now, we need to understand the factors controlling carbon fluxes over timescales to comprehend how terrestrial ecosystems will respond to upcoming decades of climate change. This paper reviews studies of year-to-year changes of NEP of terrestrial ecosystems and shows how NEP responds to present climate fluctuations. It also reports long-term and intensive studies of carbon cycling in temperate regions, not only eddy covariance but also biometric measurements, conducted at Harvard and Takayama Forests. These temperate forests are not climax forests at non-equilibrium stages due to human disturbances in the mid-20th century. Successional changes of ecosystem structures that respond to disturbances greatly affect ecosystem functions such as NEP. Therefore, we need to understand not only ecosystem responses to climatic factors, but also age and structural effects on NEP. Long-term monitoring of ecosystems is necessary to determine how successional dynamics affect carbon cycling in mountainous forest regions of Japan.