The perennial soybeans (Glycine subgenus Glycine), are the sister group of the annual cultivated soybean (G. max). Among the approximately 20 species are diploids and polyploids, the former confined to Australia and neighboring islands and the latter more widespread. Although most subgenus Glycine species reproduce predominantly by selfing in cleistogamous flowers, phylogenetic evidence exists for reticulate evolution throughout the history of the subgenus. The entire genus is a paleopolyploid, and could possibly be allopolyploid, though there is as yet no evidence for a hybrid origin. Incongruence among the major nuclear genome groups in nuclear and chloroplast gene trees can be explained by several ancient introgressions. Within the B-genome group there is substantial incongruence between chloroplast and nuclear single copy gene trees that is explained better by introgressive hybridization than by stochastic sorting of ancestral lineages. Several allopolyploids originated by hybridization among a subset of genome groups to form a single large interconnected polyploid complex. A number of allopolyploid combinations have arisen recurrently, some bidirectionally. Some recurrent polyploids show evidence of lineage recombination, indicating that their populations comprise a single biological species. Neopolyploidy has involved hybridization among a subset of subgenus Glycine genome groups, and appears to have occurred recently, whereas hybridization at the diploid level has occurred throughout the history of the group.