<p>Mitochondrial genomes play essential roles in plant energy metabolism and evolution, yet their structural complexity and diversity in plants remain poorly understood. This study aims to address the question by analyzing four newly assembled <i>Mentha</i> mitochondrial genomes (<i>M. longifolia</i>, <i>M. suaveolens</i>, <i>M. pulegium</i>, and <i>M. requienii</i>), which serve as valuable genomic resources for phylogenetic and evolutionary studies. Comparative analyses revealed structural diversity, codon usage bias, extensive RNA editing, and abundant repetitive sequences driving genomic rearrangements in the four mitochondrial genomes. Chloroplast-derived DNA fragments were dynamically integrated into the four <i>Mentha</i> mitochondrial genomes, highlighting ongoing interorganellar DNA transfer between plastids and mitochondria. Phylogenetic reconstructions based on mitochondrial, nuclear, and chloroplast genomes exhibit considerable discordance, reflecting complex evolutionary processes such as hybridization, introgression, and allopolyploidization within the genus. In conclusion, the structural diversity, codon usage bias, and ongoing interorganellar DNA transfer observed in <i>Mentha</i> mitochondrial genomes underscore their dynamic evolutionary nature. The discordance among mitochondrial, plastid, and nuclear phylogenies reflects complex evolutionary processes (possibly hybridization and allo-polyplodization) of <i>Mentha</i> species. These findings enhance the understanding of the mechanisms underlying the complexity and diversity of <i>Mentha</i> species and provide broader insights into the evolution of plant mitochondrial genomes.</p>