In order to investigate the effects of boron application on seedling growth and yield of different genotypes of canola to boron application, an experiment was conducted in 2005-2006 at Ramin Agricultural and Natural Resources University, Kouzestan province, Iran. The pots were arranged in a randomized complete block as a split-plot design with two B rates (0 and 10mgH2B03/kg Soil) and six genotypes of canola (Hyola 401, Hyola 407, PF, PF 7045/1095, RGS and Option). All treatments were replicated three times. The results showed that the boron application increased the number of seeds per pod, 1000 grain weight, seed yield and biological yield significantly but increased the number of pods per unit area non-significantly.Between different genotypes of canola there was no difference in seed and biological yield, but HI, number of pods per unit area and 1000 grain weight varied significantly between different genotypes of canola. Between different genotypes of canola, root dry weight, shoot dry weight and root/shoot ratio in seedling growth stage varied significantly, but no difference in leaf boron content in early flowering stage was observed. With boron application, root dry weight, shoot dry weight and root/shoot ratio in seedling growth stage increased significantly. Cultivars RGS and Option with boron application showed lower seed yield significantly which indicates canola genetic variation in response to boron application.