Biodiversity in European agricultural landscapes is at stake, with many once widespread species now being endangered, extinct or confined to few areas. So is the Danube Clouded Yellow butterfly, Colias myrmidone, with few populations left in three Eastern European countries, namely Poland, Slovakia and Romania. However, ecological understanding of its relationship to environmental conditions and land-use practises is piecemeal. Here, we quantify the environmental conditions determining the distribution of C. myrmidone for some of its last known strongholds in Romania. We performed random stratified searches for the butterfly and its hostplant Chamaecytisus sp. in and around three Natura 2000 sites in Transylvania, which we have subdivided into 100 × 100 m grid cells. During 2016–2019, we observed C. myrmidone in 1765 grid cells. Logistic regression modelling related the presence of C. myrmidone and its hostplant to temperature, precipitation, slope, distance to forest, land cover and aspect. The butterfly was more likely to occur with higher temperatures and higher precipitation and was associated with flat and slightly inclined slopes near forests. Furthermore, the probability was higher on grasslands, pastures and in agricultural mosaic landscapes compared to arable land and forests, with a preference for an Eastern and north-western aspect. We extrapolated these findings to predict potential other areas of occurrences with a precision of 91%. Our resulting map may be useful for conservationists to prioritise assessments and area-based conservation strategies for safeguarding this highly endangered species also outside the designated Natura 2000 sites.