The genetic structure of the “Badda” common bean cultivated at Polizzi Generosa, a village of Sicily (Palermo, Italy), was investigated using biochemical and molecular markers. Seed storage protein analysis by using SDS-PAGE, confirmed the attribution to the Andean gene pool. Simple Sequence Repeats (SSR) (or microsatellite) molecular markers provided useful information on genetic variation and relationships between “Badda bianco” and “Badda nero” morphotypes. Based on SSR data, the nine accessions examined were grouped in three sub-clusters. The first sub-cluster included all the accessions belonging to the “Badda bianco”. Conversely, “Badda nero” was constituted by two well-distinguished sub-clusters, one of them forming a well-separated branch. This result suggests that two constitutive nuclei contributed to the genetic background of “Badda nero”. Moreover, technological and nutritional data evidenced a good seed protein content (mean value 240.7 g kg−1) and differences in seed hydration rate among accessions. Knowledge of genetic structure appear to be fundamental in planning safeguard strategies of an appreciate landrace such as the “Badda” bean.