Agricultural areas, such as cereal cultivations, that support species of European and/or national conservation concern are considered as ‘High Nature Value’ farmlands (HNVf) and are very important for the preservation of biodiversity in Europe. The lesser kestrel Falco naumanni is a migratory falcon breeding largely in the HNVf of the Mediterranean basin. The main cause of its decline in Europe has been habitat loss and degradation as a result of agricultural intensification driven largely by the EU Common Agricultural Policies (CAP). In Greece, its population dropped by about 50% since the 1970s and its preferred habitats have shrunk. The aim of this study was to assess habitat preferences of breeding Lesser Kestrels in agro-ecosystems of Greece and relate these habitats to HNVf for conservation purposes. The study area is located in the plain of Thessaly, Central Greece, holding the main lesser kestrel breeding populations in the country, where dry cereal crops have been significantly depleted over the past decades. Species distribution models were developed with generalised additive models for the analyses. Predicted probability of lesser kestrel occurrence was found to be positively associated with farmed landscapes of dry cereal cultivations. Other important predictors were cultivated irrigated farmland and landscape heterogeneity. Main results of the statistical models agree with the findings of other habitatbased studies that highlight the importance of low-input farming systems, that is, HNVf, for safeguarding vital Lesser Kestrels habitats in their breeding grounds in the Mediterranean. A key conservation priority for conserving species dependant on HNVf is the maintenance of those low-input farming systems and the implementation of a greener CAP that would promote environmental-friendly farming practices to preserve and enhance biodiversity in the agro-ecosystems of Europe.