Infection with ostreid herpes viruses (OsHv-1) have been causing mass mortalities and reeking havoc on production areas world wide. The resulting production losses have sparked several selective breeding programmes trying to improve resistance to infection. Recent studies showed however that there is genetic variation in OsHv-1 strains between different outbreak areas. Furthermore, it has been suggested that secondary infection by pathogenic bacteria contribute substantially to the observed mortalities. Together this means that the disease differs between regions suggesting that also the genetic determinants of resistance differ them. To test assess the role of environmental variation in disease we employ whole genome sequencing of pools of individuals (poolseq) pairing before and after mortality samples collected during mass mortalities across Europe (France, Germany, Ireland, Norway). We identified 67-109 outlier loci for all pairwise comparisons that showed either signatures of selective sweeps (fixation of major alleles) or allelic pull-ups (increase of minor alle frequency). While we could identify single nucleotide polymorphisms (SNPs) located in close genomic proximity for most pairwise comparisons, that also matched previous QTL-studies, the majority of outlier loci were unique to each location. This supports the polygenic architecture of OsHV-resistance, but also highlights the substantial selective differences between locations. Since the shared outlier loci probably only explained a relatively small variation in resistance, breeding programs should aim at location specific resistance rather than general resistance.