Abstract Cereal rye ( Secale cereale ) is a grain, forage, and cover crop, with specific regional production practices. Maintaining regional varieties is challenged by rye reproductive biology, as wind pollination may dilute varietal distinction. Similarly, breeding new population varieties for regional needs lacks efficiency gains seen in other grains. We sought to address the challenges in maintaining and breeding rye population varieties in the Southeastern United States, where rye is a forage and cover crop, with emerging grain markets. Genetic and phenotypic variation within and between populations was characterized to determine varietal differentiation and test the efficacy of genomic selection for population improvement. Using 15 Southeastern rye accessions and eight breeding populations, we genotyped and phenotyped more than 500 individuals and found that most phenotypic and genetic variation is within rather than among accessions. Latitude of variety source, but not end use, contributed to intervarietal variation for heading date, but not traits associated with seed yield. Genomic prediction accuracy was moderately high ( r  > 0.3) for most traits, but within‐population prediction accuracy was more variable, with only some populations having nonzero within‐population prediction accuracy. This work establishes the inter‐ and intravarietal differentiation in Southeastern rye accessions, and demonstrates viability of genomics‐enabled population improvement for regional varieties.