The Chilean common bean (Phaseolus vulgaris L.) belongs to the cultivated race Chile and its origin is presumably Andean. The objective of this study was to identify the origin of a group of Chilean accessions based on their genetic relationship with wild material from the Mesoamerican and Andean common bean gene pool. To achieve this objective, universal primers of chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) were used to detect polymorphism using Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP). Thirty-two genotypes were analyzed, including wild material from Mexico, Ecuador, Peru, Bolivia, and Argentina, as well as Chilean cultivated genotypes belonging to endemic Chilean accession types (Tórtola, Coscorrón, and Cuyano) and naturalized commercial lines (Frutilla, Bayo, Manteca, and Blanco grande). Results showed a low level of polymorphism for cpDNA (23%) and mtDNA (24%) in wild and cultivated Chilean common bean accessions. Some universal primers and restriction enzyme combinations were more efficient than others in detecting polymorphism. The Chilean materials were closely related to wild accessions collected in Argentina, Bolivia, and Peru indicating their Andean origin. The wild accessions from Ecuador were located in a intermediate position between the Mesoamerican and Andean accessions.