Background In Argentina, most poplar plantations are located at the Parana River Delta. Climate change models indicate an increase of flooding events for the next decades in this area. Therefore, poplar genotypes with a higher flooding tolerance will be needed for the forest activity. Whether this aim is achieved through traditional breeding or biotechnological developments, it will be important to gain a better understanding of poplar responses to flooding at physiological, biochemical and molecular levels. In a previous work, we characterized the growth and morphological responses of several poplar clones to 35 days of flooding of the root system [1]. From this group, we selected two Populus deltoides clones with different growth responses to flooding: Alton and Stoneville 67. In clone Alton, above ground growth is not affected by flooding, while in Stoneville 67 growth is reduced after the second week of flooding. In the present work, our aim was to identify mechanisms underlying the differences in growth responses to flooding between the two clones. We characterized physiological and biochemical responses in roots and leaves, during a flooding period of 28 days, followed by an after flooding period of three weeks.