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The lima bean (Phaseolus lunatus) has been cultivated in Brazil since pre-colonization times and remains an important source of food and income for small farmers. Nevertheless, the species has not been extensively studied in this country. We assessed the genetic diversity of 183 lima bean landraces collected from different regions of Brazil, maintained by Embrapa, the Brazilian Government Agricultural Research Corporation. Twelve microsatellite markers were used, and seven morphological descriptors were applied. The genetic parameters suggested high diversity of the Brazilian collection of lima beans, with a mean gene diversity of 0.68 and number of alleles varying from 5 to 15 among sites. Based on a Bayesian model using molecular data, three subpopulations were identified in the sample: one predominantly from the Andean gene pool of the species (large seeds, mean 100-seed weight of 80g), and two predominantly from the Mesoamerican pool (both groups with a mean 100-seed weight of 34g). Another large group was composed of accessions classified as potential hybrids among the different sub-populations. All the accessions collected in the Krahô indigenous reserve were allocated in the Andean sub-population, and these indigenous accessions represented most of this Andean group. All the three sub-populations identified included accessions collected from far-apart sites in different geographic regions of Brazil. There was considerable introgression between the Andean and the Mesoamerican gene pools of cultivated P. lunatus. [ABSTRACT FROM AUTHOR]