Common bean is a species resulting from at least two, geographically distinct domestications from wild gene pools that had diverged prior to domestication. Furthermore, subsequent to domestication, the two domesticated gene pools each diverged into three to four ecogeographic races. Thus, common bean is a potentially strongly structured species at least based on analyses conducted so far with some phenotypic traits, such as leaf and seed size, and molecular markers, including seed proteins, allozymes, RFLPs, RAPDs, AFLPs, and more recently, microsatellites and DNA sequences. We will present data comparing the structure pattern of common bean revealed with some of these markers and determine to what extent the existing structure affects linkage disequilibrium in wild vs. domesticated types, between the two major gene pools, and among races within gene pools. Such information is important in determining the strategy for linkage disequilibrium mapping in common bean.