Structural variants (SVs) are typically defined as genetic polymorphisms that affect >50bp of sequence, including deletions, insertions, inversions, duplications, and translocations. While SVs are an important source of genetic variation and an important cause of inter-individual differences, they have been neglected in genetics studies compared with SNPs. Here, we defined the SV landscape in European seabass (Dicentrarchus labrax), a high value European aquaculture species. We used whole genome sequencing (WGS) in 90 animals to identify 21,428 high-confidence SVs using an established pipeline, with rigorous filtering and manual curation of every SV. These SVs were annotated to estimate potential effects on genes. Integrating SVs and SNP data generated previously, we imputed the SVs for 990 fish with phenotype data for viral nervous necrosis (VNN), one of the main infectious diseases in European seabass, allowing a GWAS analysis using the SVs. In GWAS, 108 (BS, binary survival) and 122 (DD, days to death) SVs exceeded genome-wide significance in a single QTL region matching previous work based on SNPs. The results will improve our understanding of the role of SVs in genetic architecture of traits relevant to aquaculture.