Based on previous studies of Marchantia polymorpha subsp. ruderalis chloroplast genomes, few sequence variations were identified. Here, we sequenced complete mitochondrial genome of Korean isolate, named as KDBI00084, for uncovering sequence variations on mitochondrial genomes. Its length is 186,196 bp and it contains 99 genes (67 protein-coding genes, 3 rRNAs, and 29 tRNAs). The overall GC content is 42.6\%. Only seven single nucleotide polymorphisms are identified grouped by two regions. Each region is covered by inverted repeats. It is valuable to understand the reason why mitochondrial genomes of M. polymorpha subsp. ruderalis have few sequence variations as same as chloroplast genome between Korean and Japanese isolates.