Phaseolus coccineus L. is a highly valuable crop for human consumption with a high protein content and other associated health benefits. Herein, 14 P. coccineus L. landraces were selected for genetic characterization: two Protected Geographical Indication (PGI) landraces from the Prespon area, namely “Gigantes” (“G”) and “Elephantes” (“E”), and 12 additional landraces from the Greek Gene Bank collection of beans (PC1–PC12). The genetic diversity among these landraces was assessed using capillary electrophoresis utilizing fluorescence-labeled Simple Sequence Repeat (SSR) and Expressed Sequence Tag (EST); Simple Sequence Repeat (SSR) is a molecular marker technology. The “G” and “E” Prespon landraces were clearly distinguished among them, as well as from the PC1 to PC12 landraces, indicating the unique genetic identity of the Prespon beans. Overall, the genetic characterization of the abundant Greek bean germplasm using molecular markers can aid in the genetic identification of “G” and “E” Prespon beans, thus preventing any form of fraudulent practices as well as supporting traceability management strategies for the identification of authenticity, and protection of the origin of local certified products.