In this chapter, we discussed the pressing issue of flooding and its threat to rice production, which serves as a crucial source of sustenance for over 3.5 billion individuals globally. Flooding is a grave environmental threat that can lead to significant economic losses in agriculture. Moreover, rice cultivation in rain fed lowland areas is particularly susceptible to flooding, affecting about one-third of the worlds cultivated rice areas. Given the gravity of the situation, flood-resistant cultivars must be developed to mitigate the problem and ensure food security for millions of people. Our discussion centres on the germination and seedling development of rice under various conditions, including oxygen deficiency and flooding. We highlight the significance of the genetic makeup in rice’s response to flooding, with a particular focus on the Submergence-1 locus (Sub1), which is responsible for regulating submergence tolerance. Additionally, we delve into the molecular and physiological processes that facilitate plant adaptation to hypoxic and anoxic environments, emphasizing the role of genes in regulating seed germination and coleoptile elongation. Our discourse also sheds light on the key regulator of transcriptional regulation in α-amylase promoters, the sugar response complex (SRC), and the role of the transcription factor MYBS1 in controlling the expression of the α-amylase gene in rice under conditions of sugar starvation. Furthermore, we emphasize the role of CIPK15 in integrating sugar- and O2-deficiency signalling during anaerobic germination in rice.