Abstract: In order to clarify the effects of selenium (Se) at different concentrations on root morphology, auxin contents and auxin-related gene expressions, an artificial climate incubator with light intensity of 300 μmol·m^-2·s^-1, 28℃/16 h in the day and 24℃/8 h in the evening was used to plant tobacco seedlings (homozygous DR5::GUS transgenic line, Yunyan 87). The root biomass, root length, lateral root number, MDA and auxin contents and the expression levels of NtYUCCA (a rate-limiting enzyme in auxin synthesis) and NtPIN (an auxin polar transport protein) gene families in transgenic tobacco were analyzed under Se treatments at concentrations of 0, 1, 5, 10 and 20 mg/L. The results showed that Se had double effects on tobacco growing. At low Se concentration (1 mg/L), the expression levels of NtYUCCA and NtPIN gene families, GUS activity, auxin content in root, biomass of tobacco plants, taproot length, lateral root number and antioxidant capacity increased, while MDA content decreased, indicating that the growing and development of tobacco were promoted. At high Se concentration (10 mg/L), auxin content and GUS activity reduced, suggesting that the growing and development of tobacco were inhibited.