Marchantia polymorpha subsp. ruderalis Bischl. & Boisselier is one of the common weeds as well as a model organism of a basal group of land plants. To understand the genetic diversity of M. polymorpha subsp. ruderalis based on geographical distribution, we completed chloroplast genome of KBDI00084 isolated from Mt. Cheonma in Korea. Its length is 120,304 bp, consisting four subregions: 80,706 bp of large single copy (LSC) and 19,788 bp of small single copy (SSC) regions are separated by 9,905 bp of inverted repeats (IRs). 134 genes (90 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated successfully. The overall GC content of the chloroplast genome is 29.0\% and those in the LSC, SSC, and IR regions are 26.6\%, 25.1\%, and 42.5\%, respectively. Only four single nucleotide polymorphisms (SNPs) are identified in KBDI00084, while that of Poland isolate presents 69 SNPs and 660 insertions and deletions. Phylogenetic trees show that four chloroplast genomes of M. polymorpha subsp. ruderalis are clustered into one clade. Taken together, the reason of low genetic diversity between Korea and Japan may be affected by human activities on M. polymorha subsp. ruderalis.