This article reviewed the recent advances in the investigation of rice allelopathy. The author discussed the advantages and limitations of several bioassay methods commonly used in laboratories for studying rice allelopathy. Relay seeding co-culture bioassay in agar (RSCA) is widely used in allelopathy research and perhaps the best method for laboratory bioassay. The author described the present status of quantitative genetics, QTL mapping, genetic diversity, and molecular ecological properties of allelopathy in rice. A discussion on the physiological process and its molecular mechanism of increased allelopathic potential in rice induced by the stress such as lower nitrogen supplies or higher densities of companied weed was also presented. Based on our proteomic studies, it appears that the increase in allelopathic potential of rice exposed to stresses is due to increased expression of enzymes involved in phenolic synthetic metabolism and decreased expression of enzymes associated with terpenoid synthetic metabolism. We also discussed the possible allelochemicals and their modes of action on the target weed. The inhibitory effect of allelopathic rice accessions on the target weed seems to be resulted from joint action of many allelochemicals with different cellular target sites. It is important to distinguish the primary effect of alleochemicals on the target weed from the secondary effect of allelochemicals when they are released into rhizosphere system and transformed by soil microorganism. Finally, the author highlighted the important issues critical to allelopathy studies in rice. Rhizosphere biological properties of allelopathy in rice and its mechanism are likely to be the key research areas worldwide. Recent development in systems biology and the systematic approaches such as genomics, proteomics and metabolomics would be expected to be used to reveal the process and its mechanism of molecular ecology on rhizospheric biology of allelopathy in rice.