Iron deficiency chlorosis (IDC) in soybean results in yield losses or in extreme cases death. Breeding for resistance has shown limited success with no cultivar having complete resistance. Mineral content of the soybean could be an indicator of the ability of the plant to withstand the effects of IDC. Iron (Fe) and zinc (Zn) concentration was examined in soybean seed and leaves. SSR, RFLP, and BARCSOYSSR markers were used to construct a linkage map used for mapping of Fe and Zn concentrations. The QTL analysis for the combined data identified one major QTL for seed Fe accumulation on chromosome 20 that explained 21.5% of the variation. This QTL was in the marker interval pa_515-1-Satt239, with marker pa_515-1 previously being used to map an Fe-efficiency QTL. This provides the first evidence of a potential genetic link between Fe-efficiency and Fe accumulation in the soybean seed.