The liverwort Marchantia polymorpha is one of model organism that representing basal group of land plants. Recently, two isolates of M. polymorpha subsp. ruderalis from Kyoto, Takaragaike-1 and Kitashirakawa-2, were sequenced and published, presenting that total length of chloroplast and mitochondrial genomes are 120,304 bp and 186,196 bp, respectively. To understand genetic diversity of M. polymorpha in detail, we sequenced Korean isolate of M. polymorpha subsp. ruderalis isolated in Mt. Cheonma (KBDI00084). Chloroplast and mitochondrial genomes of KBDI00084 were successfully rescued from raw reads generated by HiSeq4000 with 350bp insertion library. Strikingly, only four from chloroplast genome (0.003\%) and seven single nucleotide polymorphisms (0.004\%; SNPs) from mitochondrial genome were identified; while 490,932 SNPs from main chromosomes (0.239\%) were identified. Two out of four SNPs from chloroplast are in matK and ndhF genes. Seven SNPs from mitochondrial genomes are in intergenic space. By sequencing more Korean isolate of M. polymorpha, we will unravel geographical genetic diversity of organelle genomes of M. polymorpha.