Selective breeding for commercially valuable aquaculture traits has yielded relatively rapid successes with aquatic, high fecundity species such as salmon and oyster. Discovering the genetic changes associated with trait evolution is an important goal for understanding biological mechanisms, and also can facilitate better predictions about likely fitness of selected strains if they escape the aquaculture farm environment. Here we refer domestication as genetic changes related to increasing ease and efficiency of culture (e.g., higher survivorship at high density or higher settlement efficiencies ). Recent investigation of fish domestication revealed that rapid adaptation to captivity could be characterized by numerous, heritable changes in gene expression . In addition, genome-wide comparison between farmed and wild fish populations has identified multiple selection sweeps indicative of adaptation to the captive environment . In comparison with fish domestication, the genetic underpinnings associated with recent domestication process in shellfish are relatively less studied . Using eastern oyster as a model, this study seeks to uncover the genomic consequences of recent domestication between wild populations and selective lines from the newly developed 600K SNP array, as well as whole genome resequencing data. Paired contrasts were made between selected strains (5 - 15 generations of breeding) and the primary natural population it was originally sourced from. Principle component analysis clearly differentiated selected lines from each other and from their natural progenitor populations. Comparisons of within population variation will be presented for these population pairs to quantify the early evolutionary consequences of selective breeding on standing genetic diversity. Genome scans for loci under selection, with tests for parallel patterns across selected strains, will be discussed with respect to selected traits in common (e.g., faster growth) versus unintentional parallel adaptation to culture.