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 FZY 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 FZY gene family in tomato is closely related to the YUC gene family in Arabidopsis thaliana. A qRT-PCR showed that SlFZY2, SlFZY3, SlFZY4-1, and SlFZY5 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 SlFZY4-2, SlFZY5, and SlFZY7 contain low-temperature-responsive elements. This study demonstrated that SlTAA5 expression was 2.22 times that of SlTAA3 in the roots, and SlTAA3 expression in the pistils was 83.58 times that in the stamens during the tomato flowering stage. Therefore, various members of the tomato FZY 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.