Mitochondria play a crucial role in plant growth, fertility, and adaptation. Sugarcane (Saccharum hybrids) represents the world's primary sugar and energy crop, while S. spontaneum and S. arundinaceum serve as valuable parental germplasm. Despite their importance, limited research exists regarding the mitochondrial genomes of sugarcane and related species. This study presents the assembly of mitogenomes from one S. arundinaceum, one S. spontaneum, and five sugarcane cultivars. Analysis revealed that these mitogenomes, encoding 33 protein-coding genes (PCGs), ranged from 445,578 to 533,662 bp, with GC content between 43.43–43.82%. The primary structures of S. arundinaceum consisted of three small rings, while S. spontaneum exhibited one ring and one linear structure, and sugarcane displayed two rings; multiple potential conformations emerged due to repeat-mediated recombination. Additionally, this research developed an intron marker SAnad4i3 capable of species differentiation. The analysis identified between 540 and 581 C to U RNA editing sites in the PCGs, with six RNA editing sites linked to start or stop codon creation in S. arundinaceum, and five sites each in S. spontaneum and sugarcane hybrids. Significantly, 30–37 fragments homologous to chloroplast DNA were identified, with S. spontaneum containing the highest number. These mitogenomes appear to have undergone substantial genomic reorganization and gene transfer events throughout evolution, including the loss of eight PCGs. This comprehensive study illuminates the genetic diversity and complexity of the Saccharum complex, establishing a foundation for future germplasm identification and evolutionary research.