Most crops cannot germinate underwater. Rice exhibits certain degrees of tolerance to oxygen (O2) deficiency for anaerobic germination (AG) and anaerobic seedling development (ASD). Direct rice seeding, whereby seeds are sown into soil rather than transplanting seedlings from the nursery, becomes an increasingly popular cultivation method due to labor shortages and opportunities for sustainable cultivation. Flooding is common under direct seeding, but most rice varieties have poor capability of AG/ASD, which is a major obstacle to broad adoption of direct seeding. A better understanding of the physiological basis and molecular mechanisms regulating AG/ASD should facilitate rice breeding for enhanced seedling vigor under flooding.