The eastern oyster (Crassostrea virginica) is a vital component of coastal ecosystems and the aquaculture industry in the United States, and the use of genomic technologies have shown promise for understanding the population dynamics of wild populations, informing restoration and fisheries management decisions, and accelerating genetic improvement in oyster breeding programs. Recent population-level genome resequencing efforts have revealed the presence of several large chromosomal inversions in the eastern oyster genome, and the genetic and phenotypic impacts of these polymorphic inversions have yet to be assessed. In this presentation, we discuss current progress towards discovery and characterization of chromosomal inversions in the C. virginica genome, as well as the potential implications for population management and selective breeding.