||Carbon isotope discrimination (∆13C) is considered as an index of leaf-level water use efficiency, an important objective for plant breeders seeking to conserve water resources. We report in rice a genetic analysis for ∆13C, leaf structural parameters, gas exchange, stomatal conductance, and leaf abscisic acid (ABA) concentrations. Doubled haploid and recombinant inbred populations, both derived from the cross IR64 × Azucena, were used for quantitative trait locus (QTL) analysis following greenhouse experiments. ∆13C QTLs on the long arms of chromosomes 4 and 5 were colocalized with QTLs associated with leaf blade width, length, and flatness, while a QTL cluster for ∆13C, photosynthesis parameters, and ABA was observed in the near-centromeric region of chromosome 4. These results are consistent with phenotypic correlations and suggest that genetic variation in carbon assimilation and stomatal conductance contribute to the genetic variation for ∆13C in this population.