Organelle genome sequence data are a valuable tool to study phylogenetic relationships and genome evolution. Low coverage whole genome shot gun sequencing provides good coverage of organelle genomes making genome-sequencing projects possible for any plant species. Despite its power, features of mitochondrial genomes such as large repeat regions, presence of promiscuous DNA and its high frequency of recombination have limited the application of next generation sequencing technology for de novo assembly of mitochondrial genomes. Using reads from whole genome 454 shotgun sequencing we developed a de novo assembly of the mitochondrial genome of Daucus carota. Development and use of a new bioinformatics tool allowed resolution of assembly ambiguity across repeat regions. Illumina reads were used to confirm the sequence and correct for homopolymer sequence errors. Preliminary annotation suggests that the use of both Roche 454 and Illumina data provided a good strategy to obtain a high quality reference genome. A complete annotation of the genome is ongoing. The strategy used in this study has broad application to explore more mt genomes, and to further investigate intra-cellular genome interaction and genome evolution.