There are very few genomic resources for the native Puget Sound (Washington, USA) oyster, Ostrea lurida. In order to aid restoration efforts of this native oyster, we have produced high-throughput sequencing data from three geographically-distinct populations found in the Puget Sound. These data provide a needed resource to aid proper management of this species during restoration.</p><p>We used a genotype-by-sequencing approach to sequence 32 individuals from each of three geographically-separated Olympia oyster populations (Dabob Bay, Fidalgo Bay, Oyster Bay).