<p>Extreme precipitation and prolonged flooding are increasingly threatening ecosystems worldwide, with waterlogging emerging as a major constraint for wheat plants, disrupting metabolic processes, particularly during reoxygenation. This study investigates the physiological and molecular responses of two newly developed wheat genotypes, Nova Bosanka (B) and Julija (J), to waterlogging for up to eight days, followed by a six-day reoxygenation period. Under waterlogging conditions, genotype J showed an efficient early antioxidant response characterised by the upregulation of <i>Cu/Zn</i> superoxide dismutase (<i>SOD</i>) and catalase (<i>CAT</i>) genes. Although genotype B showed a stronger induction of the peroxidase (<i>POX</i>) gene, accompanied by an increase in hydroxycinnamic acid levels, transient oxidative stress occurred, as indicated by decreased glutathione levels and increased lipid peroxidation. However, during reoxygenation, both genotypes activated ROS-detoxifying genes <i>(POX</i>,<i> Cu/ZnSOD</i>,<i> MnSOD</i> and <i>CAT</i>), emphasising the importance of H₂O₂ regulation in the post-hypoxia phase. In addition, lactate dehydrogenase (<i>LDH1)</i> gene expression was strongly induced after reoxygenation in both genotypes, indicating its potential role in post-hypoxic metabolic recovery. On the other hand, temporal and genotype-specific differences in ethylene-responsive transcription factors (<i>ERF)</i> gene expression (early <i>ERF RAP2.3</i> in J, <i>ERF1</i> in B) were observed during waterlogging. Our study reveals a genotype-specific and complex interplay between antioxidant defence and ethylene signalling during waterlogging and subsequent reoxygenation in wheat, ultimately aiming to improve crop flooding tolerance.</p>