Many phylogeographic studies of various tree species have been conducted to elucidate the locations of refugia and the colonization patterns during the Pleistocene. However, only a few large-scale phylogeographic studies have been conducted on herbaceous plants, especially scarce on herbs that are adapted to disturbance. Artemisia indica is a fast-growing perennial herb found in open habitats. To examine the basic information on the genetic structure of this species, we investigated the chloroplast DNA variation within and among populations across Japan. We detected 26 haplotypes in 604 individuals from 28 Japanese populations. The haplotype A1 had wide geographic distribution, and its close relatives were locally present. Some putative ancestral lineages were found mainly in the Kyushu region. This may be because several lineages migrated from the Eurasian continent to the northern coast in Kyushu via the Korean peninsula during the Pleistocene, and the A1 haplotype expanded northward, whereas others remained in southern areas. Phylogenetic distant haplotypes were present mainly in the Kanto region. Because the geographic distribution pattern of these haplotypes in this region is believed to be unnatural, these haplotypes may be derived from commercial sources for re-vegetation during the last few decades.