Crop genetic vulnerability has again become a topic of concern because of the arrival of soybean rust in North America.  Crop genetic vulnerability is the condition of being broadly susceptible to attack by pests and is assumed to be proportional to genetic uniformity.  Genetic variability and apparent genetic vulnerability of North American soybean at the DNA sequence level was assessed in fragments from 102 genes in each of 26 accessions of G. soja, 52 Asian Landraces, 17 Ancestors of North American cultivars and 25 “Elite Cultivars”.  Aligned sequence included 22 kb of coding sequence, 11 kb of UTR, 18 kb of introns, and 2 kb of genomic sequence totaling 53 kb.  These data indicated that the low diversity amongst the Elite Cultivars arose not only from diversity loss during domestication of its progenitor G. soja, but also because G. soja itself has low diversity.  Indeed, the diversity in G. soja when expressed as nucleotide diversity (θ=0.00235) is lower than in other crop progenitors.  Domestication further reduced diversity.  The Landraces (θ=0.00115) retained only 49% of the variability present in G. soja.  Contrary to widely held assumption, the low diversity of North American soybean is not due to the introduction of a few individuals to North America followed by further elimination of variability via selection.  The 17 Ancestors (θ=0.00100) retained 87% of the diversity of the Landraces and the Elite Cultivars (θ=0.00083) retained 83% of the diversity of the Ancestors.  Thus, 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 indicated 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.