Knowledge of the genetics of leaf chlorophyll content (LCC) at tillering and heading stages should help develop rice varieties with high photosynthetic ability. In this study, 182 backcross-recombinant inbred lines (BIL), derived from Koshihikari (japonica)/Kasalath (indica)//Koshihikari, were used to identify quantitative trait loci (QTL) for LCC at the tillering and heading stages of rice. Continuous variation and transgressive segregation for LCC were observed in the BIL population, indicating that LCC was a quantitatively inherited trait. Seven QTL for LCC were identified and mapped to chromosomes 1 (two QTL), 2, 3, 4, 6, and 8, which individually accounted for 5.1 to 14.8% of the total phenotypic variation. Three QTL (qLCC-1-1, qLCC-1-2 and qLCC-4) were common between the tillering and heading stages. The alleles at four QTL (qLCC-1-1, qLCC-1-2, qLCC-2, and qLCC-8) from Koshihikari and the alleles at the other three QTL (qLCC-3, qLCC-4 and qLCC-6) from Kasalath increased LCC. The tightly linked molecular markers flanking the QTL detected in this study should be useful in improving photosynthetic ability in rice.