Abstract: In order to reduce production cost and address environmental pollution due to heavy use of chemical nitrogen fertilizer for high rice yield, there is a strong interest in developing high efficiency of rice rhizosphere associative nitrogen fixing system. For this purpose, it is important to breed rice varieties with strong associative nitrogen fixing ability to get high nitrogen fixing efficiency bacteria strains. A strain with high nitrogen fixing efficiency has been isolated in our previous study. In order to breed such rice varieties, we studied the genetic basis of rice associative nitrogen fixing ability. A recombinant inbred lines (RILs) population consisting of 241 recombination lines, derived from an elite combination, Zhenshan97Minghui 63 and two strains of high efficient nitrogen-fixing bacteria named as W12 and FY were used in this study. The strain W12 with higher nitrogenase activity was isolated from cotton rhizosphere in Egypt and the strain FY was provided by Chinese Academy of Agricultural Sciences. An improved spermosphere mode method was use to detect the nitrogenase activity of each RILs line associated with each nitrogen-fixing bacteria strain. Based on the molecular marker linkage map of RILs population, the QTLs mapping of associated nitrogen fixation ability in rice rhizosphere was done by the method of QTL interval mapping using the program MAPMAKER/QTL. A QTL for each strain was detected at tow independent intervals on the chromosome 2, separately. The qWNFA-2 for W12 is flanked by interval RM208～RM207 with LOD score 2.81 accounting for about 5.4% of the total phenotypic variance and the qFYNFA-2 for FY is flanked by interval R712～RM324 with LOD score 2.98 accounting for about 5.8 % of the total phenotypic variance. According to this result, it was supposed that rice rhizosphere associative nitrogen fixing ability associated with two strains was controlled by different genes.