Conservation of agrobiodiversity is a major concern worldwide. Several strategies have been designed and programmed to reduce biodiversity erosion due to anthropic and non-anthropic causes. To this end, we set up a multidisciplinary approach based on the genetic analysis of selected cultivars and recognition of the environmental parameters. We genotyped the sweet cherry cultivars of Campania region in southern Italy by using simple sequence repeats and further investigated them by cluster analysis, disclosing a homogeneous genetic constitution, different from that of commercial accessions. By structure analysis we identified three distinct genetic clusters, each characterized by common and distinct alleles. Survey of the cultivars' geographical distribution by quartic kernel function identified four preferred districts further characterized for soil origin, pedologic, agronomic features and urbanization impact. We correlated these environmental parameters, typical of the identified areas, with the three genetic pools and found a statistically significant association for each cluster. When we overlaid the cultivation traditions and cultural heritage, we found they have a dominant role; on these premises, we generated new territorial maps. In conclusion, we propose a novel methodological approach based on molecular, geo-pedological and cultural parameters with the aim to recognize biocultural refugia and preserve endangered or valuable cultivars.