Abstract: In this study, the characteristics of flat pod rate(FPR) among 1554 soybean accessions over 3 years were identified, and the related genetic loci controlling FPR were mapped by genome-wide association study(GWAS). The results showed that environments(years), genotypes and their interaction significantly affected FPR. The range of FPR was from 0.00% to 70.30% with a mean of 4.30%. 75% of the accessions had FPR less than 5.34%, 94.5% less than 10%. Six elite accessions with zero FPR were screened out. The accession-based broad sense heritability of FPR was 0.51. FPR was correlated with domestication and improvement related traits and landraces usually had lower FPR than improved cultivars. Six candidate loci associated with FPR were distributed on 5 chromosomes. Among them, qFPR-3 on chromosome 18 could be detected by 2 GWAS analysis methods simultaneously. A candidate gene, Glyma.18G085900, which codes a pentatricopeptide repeat(PPR) superfamily protein and its homologous gene in Arabidopsis is associated with embryo development is determined for qFPR-3 by haplotype analysis.