Background:Ferrous iron (Fe) and zinc (Zn) at high concentration in the soil cause heavy metal toxicity andgreatly affect rice yield and quality. To improve rice production, understanding the genetic and molecularresistance mechanisms to excess Fe and Zn in rice is essential. Genome-wide association study (GWAS) is aneffective way to identify loci and favorable alleles governing Fe and Zn toxicty as well as dissect the geneticrelationship between them in a genetically diverse population.Results:A total of 29 and 31 putative QTL affecting shoot height (SH), root length (RL), shoot fresh weight (SFW),shoot dry weight (SDW), root dry weight (RDW), shoot water content (SWC) and shoot ion concentrations (SFe orSZn) were identified at seedling stage in Fe and Zn experiments, respectively. Five toxicity tolerance QTL (qSdw3a,qSdw3b,qSdw12andqSFe5/qSZn5) were detected in the same genomic regions under the two stress conditionsand 22 candidate genes for 10 important QTL regions were also determined by haplotype analyses.Conclusion:Rice plants share partial genetic overlaps of Fe and Zn toxicity tolerance at seedling stage. Candidategenes putatively affecting Fe and Zn toxicity tolerance identified in this study provide valuable information forfuture functional characterization and improvement of rice tolerance to Fe and Zn toxicity by marker-assistedselection or designed QTL pyramiding.