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The establishment of the Natura 2000 network in Romania constitutes a turning point for the policy on biodiversity conservation in this country. The presence of human communities in certain Natura 2000 areas determines complex interactions between social and ecological systems, particularly in the case of High Nature Value farmlands that are assigned to this network of protected natural areas. A large part of Romania’s biodiversity depends on traditional farming systems that are under pressure from either agricultural intensification or land abandonment, which reflects socio-economic changes that have pushed rural households into developing new livelihood strategies. This paper explores the particular context of traditional rural communities from Southern Transylvania which is a High Nature Value farmland area largely included in the Natura 2000 network. We conducted an empirical analysis that focused on two main issues. The first was applying quantitative methods aimed at identifying the linkages between livelihood capitals and livelihood strategies of people living in Natura 2000 areas. The second was analyzing differences in local development levels which correlate with the share of territorial administrative units belonging to Natura 2000 areas. Our results are based on questionnaire and interview data collected from 40 rural administrative-territorial units within Southern Transylvania as well as on mapping land use changes using Landsat satellite images of 1985, 2003 and 2015. The results indicate that rural communities living in Natura 2000 areas turn to migration as an additional household strategy besides usual on-farm and off-farm activities, leading to rural shrinkage and farmland abandonment.