Interspecific hybridization is widespread for sunflowers, both in wild populations and commercial breeding. One of the most common species that can efficiently cross withHelianthus annuusis the Silverleaf sunflower—Helianthus argophyllus. The current study carried out structural and functional organization analyses of mitochondrial DNA inH. argophyllusand the interspecific hybrid,H. annuus(VIR114A line) ×H. argophyllus. The complete mitogenome ofH. argophylluscounts 300,843 bp, has a similar organization to the mitogenome of cultivated sunflower, and holds SNPs typical for wild sunflowers. RNA editing analysis predicted 484 sites inH. argophyllusmitochondrial CDS. The mitochondrial genome of theH. annuus×H. argophyllushybrid is identical to the maternal line (VIR114A). We expected that significant rearrangements in the mitochondrial DNA of the hybrid would occur, due to the frequent recombination. However, the hybrid mitogenome lacks rearrangements, presumably due to the preservation of nuclear–cytoplasmic interaction paths.