This research was conducted to investigate the relationship between different traits, detecting factors affecting this relationship and to identify components of seed yield in canola under drought and normal conditions. Twenty eight canola cultivars were evaluated for morphological, agronomic and physiological traits under water stress and normal irrigation according to a randomized block design at Isfahan University of Technology research farm during 2008-09. Results showed that proline content had significant correlation (0.42) with seed yield under drought stress and possibly can be used as an indirect selection index for drought tolerance. In non-stress condition seed yield had significantly positive correlation with traits number of pods per plant, number of seeds per pod, number of pods per plant, number of pods per unit area while in stress condition no correlation was found between yield and number of pods per plant. Relative water content (RWC) was positively correlated with seed yield in both moisture environments. Stepwise regression revealed that number of seed per pod, number of pod per unit area and 1000-seed weight had the greatest contribution in justifying seed yield under non-stress condition. Under drought condition, 1000- seed weight, number of pods per plant, number of seed per pod and days to heading had the greatest contribution. Cluster analysis based on all measured traits under non-stress and stress conditions divided cultivars into three groups. Cultivars which had the most genetic distance could be used as an appropriate candidate for breeding programs to improve and produce new cultivars with higher drought tolerance.