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Sepal is an important component of the tomato flower and fruit that typically protects the flower in bud and functions as a support for petals and fruits. Moreover, sepal appearance influences the commercial property of tomato nowadays. However, the phenotype information and development mechanism of the natural variation of sepal morphology in the tomato is still largely unexplored. To study the developmental mechanism and to determine key genes related to downward sepal in the tomato, we compared the transcriptomes of sepals between <i>downward sepal</i> (<i>dsp</i>) mutation and the wild-type by RNA sequencing and found that the differentially expressed genes were dominantly related to cell expansion, auxin, gibberellins and cytokinin. <i>dsp</i> mutation affected cell size and auxin, and gibberellins and cytokinin contents in sepals. The results showed that cell enlargement or abnormal cell expansion in the adaxial part of sepals in <i>dsp</i>. As reported, auxin, gibberellins and cytokinin were important factors for cell expansion. Hence, <i>dsp</i> mutation regulated cell expansion to control sepal morphology, and auxin, gibberellins and cytokinin may mediate this process. One <i>ARF</i> gene and nine <i>SAUR</i> genes were dramatically upregulated in the sepal of the <i>dsp</i> mutant, whereas seven <i>AUX/IAA</i> genes were significantly downregulated in the sepal of <i>dsp</i> mutant. Further bioinformatic analyses implied that seven <i>AUX</i>/<i>IAA</i> genes might function as negative regulators, while one <i>ARF</i> gene and nine <i>SAUR</i> genes might serve as positive regulators of auxin signal transduction, thereby contributing to cell expansion in <i>dsp</i> sepal. Thus, our data suggest that 17 auxin-responsive genes are involved in downward sepal formation in the tomato. This study provides valuable information for dissecting the molecular mechanism of sepal morphology control in the tomato.