Iron (Fe) toxicity is a major constraint in lowland rice. Because of its higher rusticity and adaptability to adverse soil conditions, the African rice Oryza glaberrima constitutes a new potential source of genes for rice improvement. This study aimed at mapping quantitative trait loci (QTLs) for resistance to Fe toxicity. A set of 220 BC3DH lines derived from the backcross O. sativa (Caiapo)/O. glaberrima (MG12)//O. sativa (Caiapo) was tested in hydroponics in the presence or absence of Fe2+ (0 or 250 mg L−1). The experiment was repeated twice independently in time. In each repetition, each line was repeated three times under each Fe2+ condition. A total of 28 QTLs were detected in 18 distinct chromosomal regions for 11 morphological and physiological traits. The single and joint composite interval mappings confirmed the interest of region RM5-RM246 on chromosome 1. Several QTLs were detected in new regions, including five QTLs and one joint QTL on chromosome 5, and one QTL on chromosome 10. Interestingly, the favorable allele for all these seven new QTLs were provided by the O. glaberrima cultivar MG12, i.e. the lesser investigated species. These QTLs corresponded to leaf bronzing index, dry weights, Fe concentration in the root-plaque system and stomatal conductance. Our results suggest that resistance mechanisms to Fe toxicity may differ between both cultivated rices and confirmed the possible interest of O. glaberrima as a source of new alleles for QTL detection and introgression in the perspective of improving rice resistance to Fe toxicity.