This data repository contains 5 Variant Call Format (.vcf) files that contain variants genotyped using a combined-species medium-density Affymetrux Axion array covering 14.950 SNPs for Ostrea edulis. The 5 .vcf files represent different combinations of 9 sampling sites and a total of 390 individuals.  Files and variables: SNPChip_TotalPanel_10407variants_AxiomAssay_Oedulis.vcf.gz: .vcf file including the total number of successfully called 10407 variants, of 390 individuals for all nine study sites (GR, OS, VD, MA, WS< H1, H2, IR, and NW). SNPChip_PrunedPanel_8403variants_AxiomAssay_Oedulis.vcf.gz: .vcf file including the total number of pruned variants (8403 SNPs), of 390 individuals for all nine study sites (GR, OS, VD, MA, WS, H1, H2, IR, and NW). SNPChip_PrunedWildPanel_9293variants_AxiomAssay_Oedulis.vcf.gz: .vcf file including the number of pruned variants (9293 SNPs), of 277 individuals from wild native (GR, OS, VD, and MA) and wild foreign (IR and NW) study sites. SNPChip_PrunedWildNativePanel_8403variants_AxiomAssay_Oedulis.vcf.gz: .vcf file including the number of pruned variants (8403 SNPs), of 194 individuals from wild native study sites (GR, OS, VD, and MA). SNPChip_PrunedSubsampledNativePanel_8403variants_AxiomAssay_Oedulis.vcf.gz: .vcf file including the number of pruned variants (8403 SNPs), of 60 individuals (12 individuals subsampled for each study site), from wild native (GR, OS, VD, and MA) and cultured native (WS) study sites.