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Background  Cotton ( Gossypium  spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of  G. hirsutum  (AD 1 ),  G. barbadense  (AD 2 ),  G. raimondii  (D 5 ) and  G. arboreum  (A 2 ), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within  Gossypium .    Results  Six  Gossypium  mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups ( G. thurberi  D 1 ,  G. davidsonii  D 3-d  and  G. trilobum  D 8 ;  G. tomentosum  AD 3 ,  G. mustelinum  AD 4  and  G. darwinii  AD 5 ), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of  G. arboreum  (A 2 ), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in  Gossypium  presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of  Gossypium . RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of  G. raimondii  and chromosome A03 of  G. hirsutum , respectively, with insertion time less than 1.03 MYA.    Conclusion  Ten  Gossypium  mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes.    Electronic supplementary material  The online version of this article (10.1186/s12864-017-4282-5) contains supplementary material, which is available to authorized users.

Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes