Unlike most parts of the European Union (EU), Southern Transylvania (Central Romania) is characterized by an exceptionally high level of farmland biodiversity. This results from traditional small-scale farming methods that have maintained extensive areas of high nature value farmland. Following the post-socialist transition, Southern Transylvania faces serious challenges such as under-employment and rural population decline, which put traditional farming at risk. With Romania's accession to the EU in 2007, Southern Transylvania became part of a complex multi-level governance system that in principle provides mechanisms to balance biodiversity conservation and rural development. To this end, the most important instruments are the ‘Natura 2000’ network of protected areas and EU rural development policy. Structured questionnaires and semi-structured interviews with town hall representatives from 30 villages in Southern Transylvania and local EU experts revealed that EU policies are often poorly aligned with local conditions. To date, the implementation of EU rural development policy is strongly focused on economic development, with biodiversity conservation being of little concern. Moreover, relevant EU funding opportunities are poorly communicated. Bridging organizations should be strengthened to foster the implementation of a rural development strategy that integrates local needs and biodiversity conservation.