Technical Abstract: A comparative genomics approach was used to investigate the evolution of a complex NB-LRR gene cluster found in soybean (Glycine max), common bean (Phaseolus vulgaris), and other legumes. In soybean, the cluster is associated with several disease resistance (R) genes of known function including Rpg1b, an R gene effective against some races of bacterial blight. We show that local duplications/deletions, recombination, and positive selection are all driving the evolution of the NB-LRR family in this region. Analysis of different domains of these NB-LRR genes revealed that the N-terminal coiled-coil (CC) domain, central nucleotide binding (NB-ARC), and C-terminal leucine-rich repeat (LRR) domains have undergone distinct evolutionary paths. Sequence exchanges within the NB-ARC domain were rare. In contrast, inter-paralogue exchanges involving the CC and LRR domains were common, consistent with both of these regions co-evolving with pathogens. Residues under positive selection were over-represented within the predicted solvent-exposed face of the LRR domain, although several were also detected within the NB-ARC domain. Superimposition of these residues on a prediction of the tertiary structure of the NB-ARC domain reveals that the majority are located on the surface, suggestive of a role in interactions with other domains or proteins. Following polyploidy in the Glycine lineage, NB-LRR genes have been preferentially lost from one of the duplicated chromosomes (homoeologues), and there appears to have been little to no sequence exchange between NB-LRR genes on separate homoeologues. The NB-LRR cluster in homoeologue 2 resides in a pericentromeric region and contains only three intact paralogues, all belonging to one ancestral NB-ARC lineage, interspersed with many NB-LRR gene fragments. In contrast, the majority of paralogues in homoeologue 1 are intact and several lineages are represented. The single orthologous region in Phaseolus contains at least as many intact paralogues as found in the two Glycine homoeologues combined, at least partially due to an increased rate of local duplications. We conclude that while polyploidization in Glycine has not driven a stable increase in family size for NB-LRR genes derived from the ancestral Rpg1b cluster, it has generated two recombinationally isolated clusters, one of which appears to be in the process of decay.