<p>Wild boars (<i>Sus scrofa</i>) have substantial impacts on island ecosystems and economies worldwide because of their rapid population growth and ability to expand their distribution. Although many studies have focused on the invasion of artificially introduced boars into islands, the natural processes of boar invasion into islands have rarely been studied. This study investigated the natural process of the recent swimming invasion of boars into Shodoshima Island in the Seto Inland Sea, Japan. We investigated whether wild boars on this island invaded from the Honshu (northern side) or Shikoku (southern side) islands. We performed mitochondrial and genome-wide single-nucleotide polymorphism (SNP) analyses of boars living on these islands. Two mtDNA haplotypes were found on Shodoshima Island, and were shared on Shikoku Island, but not on Honshu Island. SNP analysis showed that boars on Shodoshima and Shikoku Islands possessed similar genomic compositions, distinct from Honshu Island, indicating invasion from Shikoku Island. These findings suggest that the two genetic lineages of boars invaded Shodoshima Island from Shikoku Island, and the population primarily expanded through the reproduction of the two ancestry lineages. This study contributes to a better understanding of the patterns of wild boar invasion into islands and the management of boars on small isolated islands.</p>