Colias myrmidone is extinct in most European countries of its historic range, and few populations remain in Poland, Slovakia, and Romania. In Romania, this butterfly occurs in traditional farming landscapes of Transylvania dominated by high nature value (HNV) grassland. Parts of these landscapes were recently designated as Natura 2000 areas. In this article, we share insights from our engagement in these Natura 2000 areas, in which agricultural intensification as well as abandonment threaten the survival of Colias myrmidone. We unravel which factors hinder the effective conservation of this rare farmland and ecotone species despite the legally binding nature of Natura 2000 and financial support for HNV grassland in Romania through the Common Agricultural Policy (CAP). Firstly, current financial incentives to maintain low-intensity agricultural practices are insufficient to avert land-use intensification or abandonment. Secondly, a lack of knowledge of the wider landscape beyond target areas limits our understanding of population dynamics and dispersal, which impedes the ability to inform conservation management adequately. Thirdly, the target areas have unclear governance arrangements regarding responsibilities and powers, which prevents transparent collaboration and management structures. To improve support for the HNV systems that are crucial for the conservation of endangered species of traditional agricultural landscapes at the local level, we recommend greater collaboration in conservation governance with small-scale farmers, co-development of management plans, and a shift toward results-based payments for conservation actions. At the EU level, we recommend adapting the CAP to genuinely support small-scale farming and to establish a pan-European monitoring scheme for indicator species of HNV farmland such as Colias myrmidone.