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Auxin is a vital phytohormone, but its synthesis pathway is poorly understood. This study used bioinformatic analysis to identify and analyze the gene family members that encode tomato auxin biosynthesis. The <i>FZY</i> gene family members encoding flavin-containing monooxygenases were retrieved from the tomato genome database. DNAMAN analysis revealed nine genes within the landmark domain WL(I/V)VATGENAE, between the FAD and NADPH domains. Phylogenetic analysis showed that the <i>FZY</i> gene family in tomato is closely related to the <i>YUC</i> gene family in <i>Arabidopsis thaliana</i>. A qRT-PCR showed that <i>SlFZY2</i>, <i>SlFZY3</i>, <i>SlFZY4-1</i>, and <i>SlFZY5</i> were highly expressed in tomato flower organs. The analysis of promoter cis-acting elements revealed light-responsive elements in the promoters of all nine members in tomato, indicating their sensitivity to light signals. Furthermore, the promoters of <i>SlFZY4-2</i>, <i>SlFZY5</i>, and <i>SlFZY7</i> contain low-temperature-responsive elements. This study demonstrated that <i>SlTAA5</i> expression was 2.22 times that of <i>SlTAA3</i> in the roots, and <i>SlTAA3</i> expression in the pistils was 83.58 times that in the stamens during the tomato flowering stage. Therefore, various members of the tomato <i>FZY</i> gene family are involved in regulating the development of tomato floral organs and are responsive to abiotic stresses, such as low temperature and weak light.