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Breeding rice with high water use efficiency (WUE) can ameliorate water shortage through water-saving irrigation. However, WUE is a complex quantitative trait and very few studies have been conducted to measure WUE directly. In this study, a recombined inbred line population derived from a cross between an indica lowland rice and upland japonica rice was used to dissect the genetic control of WUE by fine-monitored water supply experiments. Quantitative trait loci (QTL) were scanned for 10 traits including heading date (HD), water-consumption per day (water/d), shoot weight gain per day (shootw/d), root weight gain per day (rootw/d), kernel weight gain per day (kernelw/d), average WUE at whole plant level (WUEwhole/d), average WUE for up-ground biomass (WUEup/d), average WUE for grain yield (WUEyield/d), average economic index (econindex/d), and average root/shoot ratio per day (ratio/d). The results show that most of the traits were significantly correlated to each other. Twenty-four QTL (LOD ≥ 2.0) were detected for econindex, econindex/d, WUEyield, WUEyield/d, WUEup, WUEup/d, WUEwhole, WUEwhole/ d, kernelw, kernelw/d, rootw, and water/d by composite interval mapping. These QTLs are located on chromosomes 1, 2, 4, 6, 7, 8, and 12. Individual QTLs accounted for 4.97%-10.78% of the phenotypic variation explained. Some of these QTLs overlapped with previously reported drought resistance QTLs detected in this population. These results provide useful information for further dissection of the genetic basis and marker-assisted selection of WUE in rice.