Selaginella tamariscina (Beauv.) Spring distributed in East Asia region including Korea used as traditional medicine. We completed chloroplast genome of Korean S. tamariscina. Its length is 126,368 bp and has four subregions: 53,213 bp of large single-copy and 47,560 bp of small single-copy regions are separated by 12,796 bp of direct repeat regions including 80 genes (61 protein-coding genes, 8 rRNAs, and 9 tRNAs). Phylogenetic trees show that Korean S. tamariscina is clustered with that of China species and 1,213 single nucleotide polymorphisms and 1,641 insertions and deletions are identified against Chinese S. tamariscina.