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Genomic structural variants (SVs) constitute a significant proportion of genetic variation in the genome. The rapid development of long‐reads sequencing has facilitated the detection of long‐fragment SVs. There is no published study to detect SVs using long‐read data from sheep. We applied a long‐read mapping approach to detect SVs and characterized a total of 30,771 insertions, deletions, inversions and translocations. We identified 716, 916, 842 and 303 specific SVs in Southdown sheep, Alpine merino sheep, Qilian White Tibetan sheep and Oula sheep, respectively. We annotated these SVs and found that these SV‐related genes were primarily enriched in the well‐established pathways involved in the regulation of the immune system, growth and development and environmental adaptability. We detected and annotated SVs based on NGS resequencing data to validate the accuracy based on third‐generation detection. Moreover, five candidate SVs were verified using the PCR method in 50 sheep. Our study is the first to use a long‐reads sequencing approach to construct a novel structural variation map in sheep. We have completed a preliminary exploration of the potential effects of SVs on sheep. [ABSTRACT FROM AUTHOR]