Abstract Genetic characterization of local populations is essential to understand how behavioral and ecological processes shape the spatial distribution of genetic variation. The eastern wild turkey ( Meleagris gallopavo silvestris ) is the most widely distributed subspecies of wild turkey; however, there remains a paucity of information on population genetics and genetic associations within winter flocks. Using a population genomics approach, we investigated the genetic structure and within‐flock relatedness of 379 wild turkeys in Louisiana, Georgia, and South Carolina, USA, during 2020‐2021. We observed that genetic clustering varied across our sampling area. At broad spatial scales, eastern wild turkeys clustered into 4 distinct genetic clusters, one each in Georgia and South Carolina, and 2 in Louisiana. We noted a greater degree of genetic separation than expected at some study sites, with an increased degree of genetic structure within one study site in Louisiana, suggesting a lack of gene flow. Furthermore, the probability of within‐flock relatedness was lowest at a study site where spring harvest of males did not occur. Within‐flock relatedness varied by sex and age relationships across study sites. Our findings provide relevant knowledge about flock demographics in wild turkeys and evidence of variable genetic structure in wild turkey populations.