Romania is one of the last strongholds of the Danube Clouded Yellow (Colias myrmidone), which is a critically endangered European butterfly species. Knowledge gaps of the ecology and the underlying drivers for its decline hinder the development and implementation of suitable management plans. Here, we investigated habitat characteristics and the social-ecological conditions in two recently established Natura 2000 sites in Romania. We conducted ecological surveys of the species’ occurrence and its habitats. We interviewed local farmers about their land-use practices and their perception of the Natura 2000 areas. Moreover, we investigated the information flow on the Natura 2000 implementation process between representatives of local governmental and non-governmental organizations. Occupied sites contained a mixture of small-scale, extensively used parcels with larger extensively grazed pastures interspersed with semi-natural elements. None of our interview partners knew previously about the designation of the respective Natura 2000 areas. People appreciated conservation efforts for the butterfly but feared restrictions that may narrow their activities and their economic benefits. Further land-use changes may threaten C. myrmidone in Romania still more in future. Fostering viability of humans and butterflies in Romania requires integration of scientific knowledge and people into management decisions. Instead of dictating rigid management schemes, such a participatory approach bears the potential to allow for spatial and temporal heterogeneity that seems to support the butterfly. Eventually, the survival of C. myrmidone depends on coordination between policies and sufficient financial support to maintain traditional and ecologically feasible management instead of detrimental developments such as intensification, abandonment and afforestation.