Arabidopsis thaliana (L.) Heynh. is a small plant species that serves as a model organism of plant biology and genetics. Here, we present the first complete mitochondrial genome of Korean A. thaliana natural isolate (named as 180404IB4), which is 368,875 bp long and contains 58 genes (33 protein-coding genes, 22 tRNAs, and three rRNAs), with a GC ratio of 44.8\%. Sixty-four single-nucleotide polymorphisms and 11 insertion and deletion regions (1,089 bp in length) are identified against the Col-0 ecotype, showing one large insertion of 1,069 bp without structural variation. Phylogenetic trees constructed from 30 conserved genes indicate that the 180404IB4 mitochondrial genome is clustered with Col-0 and three East Asian ecotypes.