| Summary: | The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus <i>Helianthus</i> is a diverse taxonomic group, including at least two economically valuable species—common sunflower (<i>H. annuus</i>) and Jerusalem artichoke (<i>H. tuberosus</i>). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles’ genetic information in <i>Helianthus</i>, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for <i>H. occidentalis</i> (281,175 bp) and <i>H. tuberosus</i> (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of <i>H. tuberosus</i>, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with <i>H. annuus</i> allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that <i>H. occidentalis</i> and <i>H. tuberosus</i> mitogenomes are much more similar to <i>H. strumosus</i> than <i>H. grosseserratus</i>.
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