Carbon isotope discrimination (螖 13 C) 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 螖 13 C, 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 脳 Azucena, were used for quantitative trait locus (QTL) analysis following greenhouse experiments. 螖 13 C 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 螖 13 C, 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 螖 13 C in this population.