Since common bean is the most important legume crop for human consumption around the world, bean breeders are challenged to increase production of beans while facing new problems like climate change. Guatemalan climbing beans have been suggested to represent race Guatemala, a newly identified race in the Middle American gene pool that may represent an untapped source of alleles for bean improvement. This study confirmed the existence of race Guatemala in the Middle American gene pool and its differentiation from other races. The low population structure found within these Guatemalan beans also makes this population ideal for discovery of candidate genes for important traits. We demonstrate that the Guatemalan population was useful to provide candidate genes for previously reported genetic factors like the V gene for flower color, and the Asp gene for seed coat luster. The important relationship between flowering time and altitudinal adaptation of beans was also emphasized.