Shortleaf pine (Pinus echinata), Missouri's only native pine species, experienced intense logging during the post-Civil War Ozark lumber boom. Although recent restoration efforts have occurred primarily on federal and state land, efforts are being made to incorporate shortleaf management strategies on private land through the distribution of 1 y old bare-root seedlings grown from seeds at the George O. White nursery in Licking, Mo. In this study we examined the genetic structure of Missouri's historic shortleaf pines to determine if geographic compartmentalization of seed stock was necessary. Using twelve polymorphic microsatellite loci, we genotyped historic shortleaf pine wood core samples from eight counties in the Missouri Ozarks and needles from seedlings provided by the George O. White nursery. Missouri's historic shortleaf pine populations exhibited high heterozygosity and no observable pattern of genetic structure between individuals of varying geographic location, diameter at breast height (DBH), or altitude. However, private alleles found in all but one of the historic populations suggest the presence of a form of genetic diversity in Missouri's shortleaf pine populations that is not present in the George O. White nursery stock. To maintain high levels of genetic diversity over the long term and prevent overrepresentation of alleles from nursery stock in reintroduced shortleaf populations, managers should consider increasing the number of individuals used as seed sources for seedling propagation.