Molecular identification of geographically close Undaria pinnatifida populations: Toward DNA ‐based branding of wild wakame

SUMMARY Undaria pinnatifida (wakame) is a brown macroalga of high economic and ecological importance in Northeast Asia, where it is cultivated and harvested from wild populations. In addition to its native range, this species has become invasive in Europe, Oceania, and South America largely through aquaculture, ballast water, and hull fouling. In Japan, wild wakame is increasingly valued as a premium product, generating a demand for DNA‐based traceability systems that can authenticate regional provenance. However, most genetic studies have focused on broad‐scale phylogeographic patterns, and the commonly used mitochondrial markers cox 3 and the intergenic region between tat C and tRNA‐Leu, as well as microsatellites, provide limited resolution for distinguishing geographically proximate populations. To address this limitation, we analyzed four populations from northern Kyushu (Jinoshima, Shikanoshima, Amakusa, and Kunisaki) using a novel mitochondrial intergenic region between cox 3 and atp 6 ( cox 3– atp 6). The novel marker exhibited higher nucleotide and haplotype diversity and enabled clear discrimination among closely situated populations, such as Jinoshima and Shikanoshima, which are separated by approximately 30 km. In contrast, most Kunisaki individuals were indistinguishable from the Amakusa haplotypes and a few were closely related to haplotypes from Shikanoshima, both located on the opposite coast of Kyushu. This pattern indicates that the Kunisaki assemblage has a composite origin dominated by affinities with Amakusa, with a minor contribution from Shikanoshima, and that recent human‐mediated introduction from other regions into Kunisaki represents one possible explanation. In conclusion, the application of the cox 3– atp 6 region as a marker improved the resolution of U. pinnatifida population structure, facilitating the distinction between geographically proximate populations and the detection of human‐mediated introductions, thereby supporting DNA‐based traceability and regional branding.