Suaeda japonica Makino is an annual herb in seashore in Korea and Japan. In this study, we presented the first complete chloroplast genome of S. japonica which is 152,109 bp long and has four subregions: 83,618 bp of large single copy (LSC) and 18,101 bp of small single copy (SSC) regions are separated by 25,195 bp of inverted repeat (IR) regions including 128 genes (83 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 36.4\% and those in the LSC, SSC, and IR regions are 34.2\%, 29.2\%, and 42.7\%, respectively. Phylogenetic trees show that two Suaeda chloroplast genomes were clustered and clade of Betoidae, Chenopodioidae, and Amarantheae are successfully resolved with high bootstrap supports. Our chloroplast genome will contribute for phylogeny of Amaranthaceae in detail.