Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial genome variety in Toona sinensis and Toona ciliata, the mitochondrial genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a mitochondrial genome map for comparison in genome structure, along with ML phylogenetic analysis with seven other Toona relatives. Results show:(1)The mitochondrial genome of Toona ciliata is 683,000 bp in length, with 45.40% GC content and circular structure, and contains 38 protein genes plus 33 transfer RNA genes, of which 33 tRNAs encode 20 amino acids. AT preference exists for MtDNA, TTT is the most frequently encountered codon, appearing 413 times, as well as the largest codon corresponding to The codon encoding the equivalent of Phe, which had the maximum content. (2)Mitochondrial genome of Toona sinensis is 638482bp in entire length, with 45.56% GC content and a circumscribed architecture, it encodes 38 protein genes and 34 transfer RNA genes, among 34 tRNAs embodying 20 amino acids. AT is preferred by mtDNA, whereas TTT, which is utilized 412 times quite often and seems to have the maximum Phe concentration, is the most frequently employed codon. (3)Both the mitochondrial genomes of Toona sinensis and Toona ciliata are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA and the number of genes. (4) In the ML evolutionary tree, Toona sinensis and Toona ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. This research provides a basis for the exploitation of Toona sinensis and Toona ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.