Suaeda japonica Makino is an annual herb found in the seashore in Korea and Japan. In this study, we presented second complete chloroplast genome of S. japonica which is 152,112 bp long and has four subregions: 83,620 bp of large single-copy (LSC) and 18,102 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, 8 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 S. japonica is monophyletic. This chloroplast genome suggests further investigation to find the relationship between morphological variations and genetic diversity.