Soybean has undergone several genetic bottlenecks.  These include domestication in Asia to produce numerous Asian Landraces, introduction of relatively few Landraces to North America, and then selective plant breeding over the past 75 years.  It is presumed that these three human-mediated events have reduced genetic diversity.  We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks.  We show that soybean has lost many rare sequence variants and had many allele frequency changes throughout its history.  Although soybean genetic diversity has been eroded by human selection after domestication, it is notable that modern cultivars have retained 72% of the sequence diversity present in the Asian Landraces.  The bottleneck with the most impact was domestication, when the low sequence diversity present in the wild species was halved and 60% of the genes exhibited evidence of significant allele frequency changes.  The level of genetic vulnerability of a crop species is assumed to be inversely proportional to its genetic diversity.  Genetic vulnerability is the condition of being broadly susceptible to attack by pests and has been of particular concern in the case of the N. American soybean crop.  The widely held assumption is that soybean breeding based upon a small number of founding Asian Landraces followed by the repeated use of a few elite cultivars in each breeding cycle has created a condition of substantial genetic vulnerability.  Our data indicate that this is not the case.  While genetic variability in North American soybean is low, this is not a result of recent human intervention but rather the intrinsically low variation in cultivated soybean.  Our data also indicate that G. soja contains many unique alleles suggesting G. soja as the reservoir of rare disease resistance alleles needed to protect the soybean crop from new disease epiphytotics.