To understand the responses of flag leaf shape in rice to elevated CO2 environment and their genetic characteristics, quantitative trait loci (QTLs) for flag leaf shape in rice were mapped onto the molecular marker linkage map of chromosome segment substitution lines (CSSLs) derived from a cross between a japonica variety Asominori and an indica variety IR24 under free air carbon dioxide enrichment (FACE, 200 μmol/mol above current levels) and currant CO2concentration (Ambient, about 370 μmol/mol). Three flag-leaf traits, flag-leaf length (LL), width (LW) and the ratio of LL to LW (RLW), were estimated for each CSSL and their parental varieties. The differences in LL, LW and RLW between parents and in LL and LW within IR24 between FACE and Ambient were significant at 1% level. The continuous distributions and transgressive segregations of LL, LW and RLW were also observed in CSSL population, showing that the three traits were quantitatively inherited under both FACE and Ambient. A total of 16 QTLs for the three traits were detected on chromosomes 1,2, 3, 4, 6, 8 and 11 with LOD (Log10-likelihood ratio) scores ranging from 3.0 to 6.7. Among them, four QTLs(qLL-6*, qLL-8*, qLW-4*, and qRLW-6*) were commonly detected under both FACE and Ambient. Therefore, based on the different responses to elevated CO2 in comparison with current CO2 level, it can be suggested that the expressions of several QTLs associated with flag-leaf shape in rice could be induced by the high CO2 level.