Agrobiodiversity is the basic resource for sustaining farmers’ livelihoods. One approach of studying sustainability of agricultural systems is to understand farmers’ management of agrobiodiversity in farmland, home gardens, and forest land, which provide bioresources for supporting households’ access to food and income. This paper presents results of the study on farmers’ management of agrobiodiversity in rice-based ecosystems in Phayao province. Three ecosystems with different production intensities were selected, namely organic rice system in rainfed lowland, integrated farming with pond system in rainfed lowland, and intensive lowland rice ecosystem serviced by communal irrigation system. Farmers managed agrobiodiversity to fulfill their needs for food security and income stability through commercial farming practice. Farmers independently managed agrobiodiversity for commercial production, but in certain circumstances, they organized as groups and partners with private sectors, local traders or farmer leaders for market access and entry. Management at community level was more pronounced in the case of managing forest resources when members of community participated in setting up rules and regulations that worked in practice. Farming livelihoods were then related to flow and combine utilization of bioresources between farmlands, homegardens, and forest ecosystems.