Plants in the field rarely face an individual stress, but rather a combination of stresses at the same time. For example, flooding or waterlogging limit oxygen in plant cells (hypoxia) and creates optimal conditions that favour pathogen attack. This thesis investigates how low O₂ regulates plant immune and defence responses. Using Arabidopsis thaliana, I established controlled “hypoxia + flg22” (HF) treatments and identified RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD) as a central point of the hypoxia/flg22 crosstalk. This is evidenced by the distinct features of the canonical flg22-triggered ROS burst, which reduces its amplitude and becomes more sustained. Furthermore, the transcriptional profile of defence genes is differentially regulated under low O₂ in a RBOHD-dependent way. Immune response-associated transcriptional and post-transcriptional outcomes of RBOHD are also regulated by hypoxia in a developmental- and light-dependent mechanism. Specifically, two hypoxia-linked modules converge on RBOHD in HF: (i) hypoxia-stabilized ERF-VII transcription factors contribute to RBOHD expression, and (ii) the PTI negative regulator, calcium-dependent kinase CPK28, controls RBOHD protein levels under HF in a light-dependent way. These layers of regulation support a model in which plants switch from an energetically expensive immune responses to hypoxia-suitable immunity through a RBOHD-dependent signalling. To investigate if similar principles occur in agricultural crop species, I screened ~100 Brassica napus varieties for waterlogging tolerance and for resistance to subsequent infection by Sclerotinia sclerotiorum. Through the study of photosynthetic parameters, waterlogging responses in B. napus were found to be highly genotype-dependent, enabling the ranking of tolerant and sensitive lines to waterlogging alone and to S. sclerotiorum infection after waterlogging. Genome-wide association and expression-marker analyses on waterlogged:control ratios highlighted a polygenic architecture but repeatedly pointed to processes that mirror the Arabidopsis work—Ca²⁺ signalling, energy/light pathways, and RNA/splicing regulators—providing candidate loci for breeding varieties that better withstand flooding-subsequent pathogen attacks. Together, the thesis shows that plants integrate oxygen status directly into immune output via RBOHD-centred modules, and that this molecular crosstalk between low O2 and defence responses is mirrored in a major oilseed crop.