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In this paper we present a methodology for the estimation of Gross Primary Production (GPP), Net Primary Production (NPP) and Net Ecosystem Production (NEP) for the main agricultural and forest ecosystems of the Lombardia Region (Italy). The MOD17 model was parameterized according to the different agro-forestry ecosystems and applied at regional scale by using satellite data with a spatial resolution of 250m. The high spatial resolution along with fine classification agro-forestry ecosystems has allowed to accurately analyze the carbon budget of an extremely fragmented and complex environment such as the Lombardia Region. Modeling results showed the role of the forests in the carbon budget at regional scale and represent important information layer for the spatial analysis and for inferring the inter-annual variability of carbon sequestration due to impacts of extreme events and recent climate change (e.g., drought, heat wave, flooding, fires).