In angiosperms, auxin phytohormones play a crucial regulatory role in fruit initiation. The expression of auxin biosynthesis genes in ovules and placenta results in uncoupling of tomato (Solanum lycopersicum) fruit development from fertilization with production of parthenocarpic fruits. We have identified two newly described genes, named Aucsia genes, which are differentially expressed in auxin-synthesis (DefH9-iaaM) parthenocarpic tomato flower buds. The two tomato Aucsia genes encode 53-amino-acid-long peptides. We show, by RNA interference-mediated gene suppression, that Aucsia genes are involved in both reproductive and vegetative plant development. Aucsia-silenced tomato plants exhibited auxin-related phenotypes such as parthenocarpic fruit development, leaf fusions, and reflexed leaves. Auxin-induced rhizogenesis in cotyledon explants and polar auxin transport in roots were reduced in Aucsia-silenced plants compared with wild-type plants. In addition, Aucsia-silenced plants showed an increased sensitivity to 1-naphthylphthalamic acid, an inhibitor of polar auxin transport. We further prove that total indole-3-acetic acid content was increased in preanthesis Aucsia-silenced flower buds. Thus, the data presented demonstrate that Aucsia genes encode a novel family of plant peptides that control fruit initiation and affect other auxin-related biological processes in tomato. Aucsia homologous genes are present in both chlorophytes and streptophytes, and the encoded peptides are distinguished by a 16-amino-acid-long (PYSGXSTLALVARXSA) AUCSIA motif, a lysine-rich carboxyl-terminal region, and a conserved tyrosine-based endocytic sorting motif.