Common bean (Phaseolus vulgaris L.) is the most important source of protein in Brazil. The crop is cultivated predominantly by smallholder farmers in a subsistence agriculture setting. A large number of landraces are cultivated in the country. This study assessed the genetic diversity of Brazilian common bean landraces integrating three approaches: genotypic information using molecular markers, phenotypic traits using field trials and environmental parameters using Geographic Information Systems (GIS). Our sample consisted of 279 randomly chosen landrace accessions from the main growing regions of beans in Brazil. Based on GIS analysis, these regions are very diverse for their eco-geographic conditions. Sixty-seven microsatellite markers spread over the 11 linkage groups, as well as phaseolin, PvTFLly, APA and four SCAR markers were used to genotype the sample. Andean and Mesoamerican common bean gene pools were clearly distinguished based on molecular analysis and on morphological traits. Overall, these two groups are cultivated in the same eco-geographic conditions. Using a model-based approach implemented in STRUCTURE, four additional sub-populations were identified in the Mesoamerican group. These sub-populations differed for some morphological traits, disease resistances, commercial seed types and eco-geographic conditions of collecting sites. Limited admixture was observed between Andean and Mesoamerican groups, while a high level of admixture was observed among the Mesoamerican sub-populations. A high degree of genome-wide association was observed among the molecular markers, confirming the high level of structure in the sample and suggesting that association mapping should be conducted in separate Andean and Mesoamerican Brazilian samples. Common bean commercial types presented significant differences for all the evaluated eco-geographic conditions of collecting sites. A landscape genome approach identified some microsatellite loci performing as non-neutral markers. Other molecular markers were correlated with environmental characteristics of the collecting sites of accessions, mainly precipitation. This study provides information on the organization of diversity of Brazilian common bean landraces, which constitute an important reservoir of diversity and rusticity for the species. The landscape genetics approach enriches the diversity overview of this crop and sets the stage for further research.