We determined the nucleotide sequences of the mitochondrial genomes of Kosena radish and SW18. SW18 has a recombinant mitochondrial genome, which includes the whole genome of Westar 222 kb (54 genes) and a total of 23kb insertions of four fragments from Kosena radish (3 genes; ORF125, trnfM and ATP1). All of the Kosena radish-derived fragments in the SW18 mitochondrial genome had sequences at their ends (ranging from 63bp to 628bp), which are identical to the sequences at their inserted sites in of the Westar rapeseed-derived mitochondrial genome. This suggests that these insertions were mediated by homologous recombination. These results confirm at the nucleotide level that a desired CMS associated-gene (orf125) along with a few extraneous genes from radish were successfully transferred.