Abstract Apples are one of the most popular and economically important fruits worldwide and have both nutritional and ornamental value. However, because of their complexity, studies on apple mitochondrial (mt) genomes have been limited. In this study, the mt genomes of Aksu Fuji and Ralls Janet cultivars were assembled, annotated, and analyzed based on a hybrid strategy using Illumina, and comprehensive comparisons of their structure, gene content, intercellular gene transfer, phylogeny, and RNA editing sites were performed. The mt genome length and gene structure of the two apple cultivars were identical (396 592 bp) and included 63 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. There were 44 and 31 mitochondrial plastid fragments (MTPTs) identified between the mt and plastid genomes of the Ralls Janet and Aksu Fuji cultivars, accounting for 1.98 and 2.19% of their mt genomes, respectively. Furthermore, there were 419 and 421 RNA editing sites were detected in Aksu Fuji and Ralls Janet, respectively. Analyses of coding usage bias, nucleotide diversity, selection pressure, and genetic distance revealed that the mt genomes of the two cultivars were highly conserved. Phylogenetic analysis of 29 Rosaceae species showed that Aksu Fuji and Ralls Janet clustered with Malus baccata and M. kansuensis. This study provides new insights into the genetics, systematics, and evolution of apple mt genomes.