•The paper reviewed the progress in rice root genetic research.•A number of genes associated with root growth or functions have been identified.•It provides an opportunity to further improve rice based on MAS. Rice is one of the most important cereal crops, feeding more than 50% population of the world. To meet the demand of increasing population, rice production has to be improved continually. As a very important part of rice plant, root system plays multiple roles in rice growth: anchorage of the plant, acquisition of water and nutrient elements, and biosynthesis of amino acids and hormones, etc. Almost all of the hot spots about rice research are associated with rice root: drought tolerance, lodging resistance, and efficient use of nutrition, the goal is to increase the grain yield with desirable seed quality. Although the understanding about rice root has been expanded in the last decades, there remain much to be done about root morphology and physiology, especially in root genetics. Rice root research is an exciting and focusing field in recent years. More and more researches on rice root genetics have been made. There is a close relation between above ground traits and underground roots, providing an alternative approach for rice genetic improvement. A number of genes associated with root architecture and physiological functions have been identified, or cloned. It provides an opportunity to further improve rice based on molecular assisted selection. Root traits improvement should be taken into account in future breeding programs in rice. However, root research is still a consuming and difficult work, because it was largely influenced by the complex underground environment. This paper reviewed the progress in rice root genetic research, and discussed its prospects.