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European agriculture and rural development policies have promoted the diversity and genetic types of autochthonous breeds to increase sheep and goat biodiversity. Agri-environmental measures to support livestock farmers, have been the main tools used by these policies over the last twenty years. The COLAUTOC, “Collection of a seed bank for native sheep and goat breeds and strategies to increase their numbers”, research project in Basilicata, Southern Italy, investigated sheep and goat farms with autochthonous breeds with results proving a reduction in the number of sheep and goat farms in general, particularly those with native breeds at risk of extinction, a clear indication of policy failure with a devastating loss of sheep and goat biodiversity. The COLAUTOC used a variety of methodological tools, including, desk analysis, focus groups, interviews, school workshops and a survey on sheep and goat meat consumption. The results indicated that a recovery in sheep and goat biodiversity could be achieved by supporting farm livestock strategies with a view to diversify production methods and activities, whilst, recognizing the value added to the territory, landscape, biodiversity and sustainability. The strategies identified by the COLAUTOC project require a local vision, using agri-environmental funds to invest in training on innovation for farms, provide tools to improve the quality of life in the rural areas, to increase communication channels to further knowledge and awareness of biodiversity. These strategies could contribute to meeting several 2030 Agenda goals.