A mapping population of 96 BC1F9 lines (Backcross Inbred Lines: BILs), derived by a single-seed descent method from a backcross of Nipponbare (japonica) / Kasalath (indica) // Nipponbare, was used to detect quantitative trait loci (QTLs) for leaf bronzing index(LBI), stem dry weight(SDW), tiller number(TN) and root dry weight(RDW) under Fe2+ stress condition in rice. Two parents and 96 BILs were phenotyped for the traits by growing them in Fe2+ toxicity nutrient solution. A total of four QTLs were detected on chromosome 1 and 3, respectively, with LOD of QTLs ranging from 3.17 to 7.03. One QTL controlling LBI,SDW,TN and RDW was located at the region of C955-C885 on chromosome 1, and their contributions to whole variation were 20.5%, 36.9%, 43.9% and 38.8%, respectively. The QTL located at the region of C955-C885 on chromosome 1 may be important to ferrous iron toxicity tolerance in rice. Another QTL for SDWand RDWwas located at the region of C25-C515 on chromosome 3, with respective contributions of 47.9% and 35.0% to whole variation. Further, two QTLs on chromosome 1 were located for RDWat the region of R2329-R210 and for TN at the region of R1928-C178. Comparing with the other mapping results, the QTL located at the region of C955-C885 on chromosome 1 was identical with the results reported previously. There is a linkage between a QTL detected under Fe2+ stress condition for stem and root dry weight and a QTL detected under phosphorus-deficiency condition for dry weight on chromosome 3.