Artemisia fukudo Makino is a salt tolerant species and contains diverse useful compounds. Here, we completed chloroplast genome of A. fukudo to understand intraspecies variations producing better useful compounds. Its length is 151,021 bp long and has four subregions: 82,761 bp of large single copy (LSC) and 18,348 bp of small single copy (SSC) regions are separated by 24,956 bp of inverted repeat (IR) regions including 125 genes (88 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of this chloroplast genome is 37.5\% and those in the LSC, SSC, and IR regions are 35.6, 30.7, and 43.1\%, respectively. Seven single nucleotide polymorphisms and 11 insertions and deletions are identified between A. fukudo isolated in different islands in the same county. Phylogenetic trees show that two A. fukudo are clustered in one clade. In addition, phylogenetic position of Artemisia annua is different from the previous study caused by lack of enough taxa. This chloroplast genome will contribute understanding of both intraspecies variations of A. fukudo and molecular phylogeny of Artemisia genus.