The international debate on biodiversity has become increasingly explicit and predominant in different disciplinary fields, requiring efforts especially on a regional scale. The future Common Agricultural Policy will be integrated and strategically connected with the objectives of the Green Deal and biodiversity protection, requiring new approaches, especially at local level. Through a review of the international literature and programming documents, the path of a significant case in the south of Italy, the Apulia region, characterized by a progressive loss of biodiversity in agriculture, will be traced. The regional government has launched a significant initiative called “custodian farmers” within the framework of the CAP in the two programming cycles 2007-2013, 2014-2020 for the protection and maintenance of biodiversity. Using a combination of different sources, we will focus on this initiative to evaluate its weight and significance at the regional level through cartographic analysis. The results will be critically analyzed and will provide reflections for the future.