Description: The repeated transgression and regression of coastlines mediated by the late Quaternary glacial–interglacial cycles make the northwest Pacific a hot spot to study marine speciation and population diversity. The red alga Agarophyton vermiculophyllum is an ecologically important species native to the northwest Pacific, capturing considerable research interest due to its wide-range invasiveness in Europe and North America. However, the knowledge of phylogeographic structure and intraspecific genetic diversity across the entire native range was still scarce. Here, we used 1,214-bp of mitochondrial cytochrome c oxidase subunit 1 (cox1) to explore phylogeographic patterns, lineage structure, and population genetic differentiation of 48 A. vermiculophyllum populations in the northwest Pacific. Our DNA data revealed overall high haplotype diversity and low nucleotide diversity and five phylogeographically structured genetic lineages that diverged significantly from each other. S-DIVA analysis showed the ancestors of A. vermiculophyllum originating from multiple areas encompassing the Japan–Pacific coast, East and South China Seas. This combined evidence indicates that A. vermiculophyllum might have survived in multiple scattered glacial refugia during the late Quaternary climate oscillations in the northwest Pacific. Such knowledge may help to better understand how palaeoclimate interacted with contemporary environments to contribute to intraspecific genetic variation and provide a new perspective for conserving natural resource of A. vermiculophyllum in the northwest Pacific.