Soil flooding is an environmental constraint that is increasingly important for forest ecosystems, affecting tree growth and regeneration. As a result, selection pressure will alter forest diversity and distribution by favouring tree species tolerant of soil oxygen deprivation. Sessile and pedunculate oaks are the most abundant oak species and they exhibit a strong differential tolerance to waterlogging. In order to gain some understanding of the mechanisms of tolerance of both species to hypoxia, we undertook the characterization of the physiological, morphological, cellular and molecular responses of both species to flooding stress. Our results indicate that pedunculate oak, the more tolerant species, succeeded in maintaining its growth, water status and photosynthetic activity at a higher level than sessile oak. Furthermore, pedunculate oak developed aerenchyma in its root cortex as well as adventitious roots. The later exhibited a strong accumulation of class1 non-symbiotic haemoglobin localized by in situ hybridization in the protoderm and in some cortical cells. In conclusion, the higher tolerance of pedunculate oak to flooding was associated with an enhanced capacity to maintain photosynthesis and water homeostasis, coupled with the development of adaptive features (aerenchyma, adventitious roots) and with a higher expression of non-symbiotic haemoglobin in the roots.