The uptake of cadmium by flue-cured tobacoo K326 and Yunyan87 and its distribution in plant cells were studied by hydroponic culture, with the comparison of biomass accumulation, chlorophyll content, root activity and microstructure changes in various treatments. The results showed that K326 decreased less than Yunyan87 in biomass, while in root activity and chlorophyll content, K326 declined more rapidly than Yunyan87. Without Cd, the size of stomas in K326 and Yunyan87 was homogeneous and the density of stomas appeared similar, whereas under Cd stress, reduced size of stomas and increased density of stomas occurred in both of the two tobacco varieties. Under Cd stress, Root diameter of K326 reduced by 35%, while no evident change was observed in Yunyan87. Cd stress migh result in abnormal root tip, and weak trichome of K326, and retarded development of trichome for Yunyan87. Cd was mainly detected in roots of the two varieties, with greatest distribution in soluble fraction of tobacco leaves. K326 exhibited more total level of Cd than in Yunyan87. Regarding biomass accumulation, Cd stress had less effect on K326 than Yunyan87. In summary, great differences of Cd tolerance exist between the two flue-cured tobacco varieties.