Genetic variation in populations, both natural and restored, is usually considered crucial for response to short-term environmental stresses and for long-term evolutionary change. To have the best chance of successful long-term survival, restored populations should reflect the extant variation found in remnants, but restored sites may suffer from genetic bottlenecks as a result of founder effects. Kankakee Sands is a large-scale restoration being conducted by The Nature Conservancy (TNC) in northwestern Indiana. Our goal was to test for loss of genetic variation in restored plant populations by comparing them with TNC’s seed source nursery and with local remnant populations that were the source of nursery seed and of the first few restored sites. Allozyme analysis of Baptisia leucantha, Asclepias incarnata, Coreopsis tripteris, and Zizia aurea showed low levels of allozyme diversity within all species and reductions in polymorphism, alleles per locus, and expected heterozygosity between remnants and restorations for all species except A. incarnata. Almost all lost alleles were rare; restored populations contained almost 90% of alleles at polymorphic loci that occurred in remnants at frequencies greater than 1%. Allele frequencies for most loci did not differ between remnants and restored sites. Most species showed significant allele frequency differentiation among remnant populations and among restored sites. Our results indicate that seed collection techniques used at Kankakee Sands captured the great majority of allozyme variation present in seed source remnant populations.