Seed transfer zones are geographically defined areas in which the interpopulation mixing of plant propagules is presumed to be genetically beneficial and unlikely to result in outbreeding depression. Crossing between individuals that differ in ploidy (the number of whole genome duplications) commonly produces sterile or mostly sterile progeny, but the landscape distribution and occurrence of polyploids is poorly known for rare plants. Seed transfer zones could provide adequate protection for rare plants with unrecognized ploidy variation provided that the distribution of ploidal variants coincides with seed zone delineations. We studied the range-wide distribution of polyploids in a threatened legume to determine whether U.S. Fish and Wildlife Service endorsed seed transfer zones have adequate protection from inadvertent mixing of individuals with non-matching ploidy.