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We studied how mitochondria affect ethylene response via modulation of CTR1 expression in cytoplasmic male‐sterile (CMS) Brassica juncea. The expression of CTR1 gene was reduced in CMS compared with male‐fertile (MF) lines. We observed that hypocotyl and root lengths were shorter than in the MF line during germination in the dark. An enhanced ethylene response was observed in CMS plants as shown by the CMS and maintainer line phenotypes treated with 1‐aminocyclopropane‐1‐carboxylic acid. The phenotype in CMS plants could be recovered to the maintainer line when treated with Ag+. One ethylene response gene, plant defensin gene, was detected to be induced in CMS. The behavior of this phenotype could be mimicked by treating the maintainer line with antimycin A that disturbs mitochondrial function, which showed reduced length of hypocotyl and roots, and resulted in similar expression patterns of ethylene‐related genes as in CMS. The reduced length of hypocotyl and roots could be recovered to the maintainer line by treatment with gibberellic acid (GA3). In addition, the GA3 content was reduced in CMS plants and in the MF line treated with antimycin A. Ethylene treatment markedly affects GA3 content; however, GA3 did not significantly affect ethylene‐related gene expression in regards to regulation of hypocotyl and root length, which suggests that ethylene acts upstream via gibberellin to regulate hypocotyls and root development. Taken together, our results suggest a link between mitochondrial modulation of the ethylene and gibberellin pathway that regulates the development of hypocotyl and roots.