The Polish rural cultural landscape is inherently linked to a special, centuries-old system that combines agricultural tradition and biodiversity. One of such environmentally, ecologically, agriculturally, historically, and culturally unique areas is the Kraków-Częstochowa Upland. Home to small agricultural holdings, this diversified mosaic is where agricultural, husbandry, craft, and local industry experience is handed down the generational chain. Developmental changes and progress are becoming the gravest threats to the area. The purpose of the paper is to assess traditional agricultural systems in the Lesser Poland part of the Kraków-Częstochowa Upland considering landscape features, agricultural biodiversity, food and livelihood security, traditional local knowledge systems, cultural values—in particular, systems of values—and social organisations that promote them. The research shows that biodiversity is entwined with cultural diversity. The vanishing of agricultural systems due to changed socio-economic conditions and environmental overprotection is a serious threat to the biological and cultural diversity in the upland. The authors employed a SWOT analysis—a tool that can investigate interactions and determine the best development strategy—to identify relationships between cultural and biological diversity.