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The differences of PBDE absorption, accumulation, and metabolism in different cultivars of the same crop are rarely explored. This study used C tracing to fully demonstrate the uptake and transformation of soil-borne BDE209 in three rice cultivars, including two indica (HHZ and YD1) and one japonica cultivars (NJ3). Results showed that about 6.9, 17.2, and 17.4% of the applied C-BDE209 were transformed to C-metabolites in soils planted with HHZ, YD1, and NJ3, respectively. The C-BDE209 and its C-metabolites in soil could be absorbed by the rice and gradually transported to its root, stem, leaf, and grain, with the total whole-plant uptake of 8.52, 4.55 and 3.43 nmol for HHZ, YD1, and NJ3, respectively. The cultivar of HHZ had the greatest whole-plant C absorption but the lowest ΣPBDEs residues in its grain, with the ΣPBDEs of 421.8, 454.2 and 967.0 ng g for HHZ, YD1, and NJ3, respectively. BDE-209 accounted for 90%, 31% and 50% of the ΣPBDEs in the grain from HHZ, YD1, and NJ3, respectively. The estimated daily intake (EDI) amounts of ΣPBDEs were 928, 1056, and 2675 ng kg bw d via consuming rice grains from HHZ, YD1, and NJ3, respectively, which were below the safe threshold limits for human consumption. This study proved the different BDE-209 absorption, accumulation and transformation in different rice cultivars, which potentially suggests the need of considering cultivar differences in assessing the dietary risks of PBDEs., This work was supported by the National Key Research and Development Plan, China (2018YFD0200101 & 2016YFD0800207) and the National Natural Science Foundation of China (21577120 & 21207113). We also thank the China Scholarship Council for funding support to PF Zhao for her visit at McGill University, Canada.