<p>Present study is aimed to comparatively investigate the response of two ploidy levels of wheat including a tetraploid (<em>Triticum turgidum</em> L.) and a hexaploid (<em>Triticum aestivum</em> L.) wheat to different durations of flooding stress. Wheat seedlings were exposed to flooding stress for 0, 3, 6 and 9 days. Results showed that all flooding treatments significantly decreased the shoot and root length, and chlorophyll content of both species of wheat. The decrease in chlorophyll content of tetraploid wheat was more than that of hexaploid one. In both species, ADH activity of root was significantly increased under flooding stress, where the increase was more in hexaploid wheat. Flooding stress did not significantly affect root and shoot water content, root porosity, and shoot protein content of any wheat species. Tetraploid and hexaploid wheat used different mechanisms for better tolerance of flooding condition, where tetraploid wheat increased the proline content but in hexaploid wheat, an increase in soluble sugar content was observed.</p>