A clear description of the certain mechanisms of cadmium (Cd) uptake and translocation in rice (Oryza sativa L.) may help to reduce Cd accumulation in rice grain. Hydroponic experiments were carried out to determine the effects of cultivation conditions (aerated and stagnant) on the uptake, translocation and subcellular distribution of Cd in relation to the morphology and anatomy of roots in two rice genotypes with different Cd accumulations in grains. Marked differences in morphology and anatomy were observed between these two genotypes under different cultivation conditions. Genotypes with low Cd accumulation in grains tended to develop fewer root tips per root surface area, larger root porosity and more mature apoplastic barriers. The stagnant cultivation condition decreased the number of root tips per root surface area but increased root porosity and accelerated apoplastic barrier formation in root tissues. Correlative Cd uptake studies revealed that rice plants with fewer number of root tips per root surface area reduced root Cd uptake ability, while mature apoplastic barriers increased root Cd retention in cell walls and the symplast. Thus, the fewer number of root tips per root surface area and the earlier formation of mature apoplastic barriers led to lower Cd uptake and translocation. The results indicated that the morphology and anatomy of roots could play important roles in Cd uptake and translocation in rice, and could be influenced by both genotype and cultivation conditions. The present results would be useful in screening and planting rice plants with low Cd accumulation.