Problem: Removing mercury from polluted soil using transgenic plants is an ideal method. However, where mercury was stored in plant cell is not clear until now. Methods: Differential centrifugation and laser scanning confocal microscopy were used in this study. Results and findings: Results showed that after mercury was absorbed by tobacco plants, most of the mercury accumulated in roots. Mercury content in root was significantly higher than that in shoot. In the seedlings cultured in MS liquid medium containing 5 μmol/L mercuric chloride, the mercury content in cell wall was 6.6 μg/g. The mercury content in cell membrane fraction was 2.1 μg/g. The mercury content in supernatant fraction was 35.1 μg/g. Most of the mercury accumulated in roots located in liquid fraction, about 15% of the mercury was attached by cell wall. Only a small part assembled in cell membrane. Most of the mercury in liquid fraction located in vacuole. This suggested that after the mercury was accumulated in plant root, most of the mercury was transferred into vacuole. There was no important cellular organ in vacuole. The toxicity of mercury in vacuole will be much lower than that in cell membrane or cellular organs. Recommendation: These results suggested that much work should be focused on how to transfer the mercury in vacuole into the above-ground tissues of the plants in the future.