Common bean is the most important legume crop for human consumption around the world. For this reason, bean breeders are challenged with increasing bean production while facing new problems like climate change. Guatemalan climbing beans have been suggested to represent a previously undefined race in the Middle American gene pool that may represent an untapped source of alleles for bean improvement that can contribute to solving production problems affecting both developed and developing countries. The genetic diversity, population structure, and genetic differentiation of two Guatemalan climbing bean collections were analyzed with ~ 45,000 SNPs markers and confirmed the existence of race Guatemala in the Middle American gene pool and its differentiation from other races. Further analysis using geospatial data, showed that elevation was an important factor when defining the population structure of race Guatemala beans.