Rice is one of the most important food crops in China， and rice production is an important guarantee for national food security. The traditional transplanting model has played an important role in increasing rice production， farmers' income， and agricultural development. With the development of social economy and changes in industrial factors， the significant reduction of rural labor forces urgently requires simplified cultivation methods. Direct seeding of rice flooding can save labor， resources， and effectively reduce weed damage， which is an efficient and economical cultivation mode with high popularization value at present. The decreased germination rate caused by hypoxia stress under submerged condition is the primary factor that hinders the application of direct seeding of rice flooding. In the abundant rice germplasm resources， there are excellent resources and genes tolerant to hypoxic stress. Exploring these excellent resources and genes tolerant to hypoxic stress and their application in developing submergence tolerant varieties suitable for direct seeding rice is the key to break through the bottleneck of popularization and application of direct seeding rice. This article reviewed the physiological characteristics， phenotyping methods， elite germplasm identification， genetic analysis， mechanism characterization of rice germinability under submerged condition and breeding application of functional genes. We expected to provide theoretical reference for deciphering the molecular mechanism of hypoxia-tolerant germination and selecting direct seeding rice varieties.