Structural variants (SVs) are one of the main sources of genetic variants and have a significant impact on phenotype evolution, disease susceptibility, and environmental adaptations. We used 73 whole genome sequencing (12x) to apply a mapping approach to identify SVs in five turkey populations. A notable degree of genetic isolation was observed between the Basilicata and Apulian populations, as indicated by principal component analysis and admixture results. A total of 11,733 SVs were detected, including 6712 deletions, 2671 duplications, 1430 inversions, and 920 translocations. The Variant Effect Predictor (VEP) analysis predicted various consequences of filtered SVs as follows: intron variants (35.8%), intergenic variants (9.6%), coding sequence variants (8.3%), downstream gene variants (7.5%), and transcript ablations (7.3%). Our functional annotation of genes overlapping with SVs was mainly enriched in recognized pathways governing positive regulation of nucleoplasm, protein binding, mitochondrion, negative regulation of cell population proliferation, identical protein binding, and calcium signaling. We produced a comprehensive SV catalog utilizing unique whole-genome turkey data. This SV catalog not only increases our understanding of genetic diversity in turkeys but also enhances our knowledge of the role of SVs in their phenotypic traits.