A selective breeding program for Crassostrea virginica was established in 1997 as part of an initiative in Virginia to address declining oyster harvests caused by the two oyster pathogens Haplosporidium nelsoni (MSX) and Perkinsus marinus (Dermo). Housed in the Aquaculture Genetics and Breeding Technology Center (ABC), the objective of the program was to develop and disseminate disease-resistant lines that would enable an oyster culture industry. Today, culture of disease-resistant cultivars accounts for more than 90% of oyster production in the state, where 28.1 million half-shell oysters and 2 billion eyed larvae were sold in 2012. Results of our line development program as of 2006 are reported. Eight ABC lines from 3 genetic groups—East Coast (EC), Louisiana (LA), and hybrids between the 2 (HY)—and 1 wild control line, were produced and tested. These 9 groups were deployed in 4 replicates across 4 Virginia sites characterized by low (Kinsale (KIN)), medium (York River (YRK) and Lynnhaven (LYN)), and high (Wachapreague (WAC)) salinity regimes. Groups were sampled routinely for survival, growth, and disease diagnosis between November 2004 and December 2006. At KIN, where salinity was low and below the threshold for MSX and Dermo, survival was 41%–46% greater than survival at the other 3 sites by the end of the trial. Where the diseases were present (LYN, YRK, and WAC), ABC lines in general had greater survival than the control, but this varied by genetic group. The EC groups had 52%–82% greater survival, the HY groups had as much as 40% greater survival, and the LA groups performed worse than the control. Poor performance of the LA groups was a result of their susceptibility to MSX, and the majority of them died before the end of the study. The genetic effects varied with site, and the rank of the lines was inconsistent, such that the best line in one site was, in some cases, one of the worst in another. Genotype-by-environment interaction is clearly driven by disease and salinity. Growth was also influenced by site, genetic group, and an interaction between them. Compared with the wild control, ABC lines were 31%, 20%, 42%, and 24% heavier at the end of the trial in the KIN, YRK, LYN, and WAC sites, respectively. However, unlike survival, the best performers were those from the LA and HY groups. Again, line rankings changed across sites. For this reason, a salinity-specific breeding strategy to develop lines that perform optimally within a salinity range has been adopted.