Our previous study showed that the auxin receptor homolog SlTIR1 in Micro-Tom tomato stimulated tomato fruit set and leaf morphogenesis. Tomato has long served as a major model for fleshy climacteric fruit development and ripening studies. Because up-regulation of SlTIR1 leads to parthenocarpic fruit, no seeds were obtained in SlTIR1 over-expression Micro-Tom tomato, limiting further analysis of SlTIR1 potential function in regulating other processes of tomato growth and development. Here, to expediently investigate the roles of SlTIR1, an antisense vector and an over-expression vector of SlTIR1 were stably transformed into Micro-Tom and Ailsa Craig tomato, respectively. Phenotypes and physiological analyses indicated that SlTIR1 not only regulates primary root growth and auxin-associated LR formation in Micro-Tom, but also stimulates abnormal seed development, so-called stenospermocarpy, in Ailsa Craig. Transcript accumulations of auxin-signaling genes related to root formation and fruit set are in accord with phenotypes in AS-TIR1 Micro-Tom and SlTIR1 up-regulated Ailsa Craig tomato. Furthermore, SlTIR1 expression is regulated by some phytohormones, such as gibberellic acid (GA), naphthaleneacetic acid (NAA), ethylene and abscisic acid (ABA), suggesting that SlTIR1 may be a key mediator of the crosstalk between auxin and other hormones in co-regulating plant growth and development.