Inoculation of plants with microorganisms may reduce the toxicity of heavy metals to plants in contaminated soils. In this study, we have shown that the plant growth promoting bacteria Methylobacterium oryzae strain CBMB20 and Burkholderia sp. strain CBMB40 from rice reduce the toxicity of Ni and Cd in tomato and promote plant growth under gnotobiotic and pot culture experiments. The bacterial strains bound considerable amounts of Ni(II) and Cd(II) in their growing and resting cells and showed growth in the presence of NiCl2 and CdCl2. In gnotobiotic assay, inoculation with the bacterial strains reduced the ethylene emission and increased the tolerance index of the seedlings against different concentrations of NiCl2/CdCl2. In pot experiments carried out with non-polluted, Ni and Cd supplemented Wonjo-Mix bed soil, the results clearly demonstrated reduction in the accumulations of Ni(II) and Cd(II) in roots and shoots, with significant increase in the plant growth attributes with bacterial inoculations compared to untreated control. Strain CBMB20 performed better than CBMB40 in reducing the heavy metal accumulations in plants. Our results suggest conclusively, that protection against the heavy metals toxicity is rendered by these bacterial strains by reducing their uptake and further translocation to shoots in plants and promote the plant growth by other PGP characteristics.