Grains of 12 accessions of Triticum timopheevii (Zhuk.) Zhuk. ssp. timopheevii (AAGG, 2n = 4x = 28) and one bread wheat cultivar Chinese Spring (CS) and one durum wheat cultivar Langdon (LDN) grown across two years were analyzed for grain iron (Fe) and zinc (Zn) concentrations. All the 12 tested T. timopheevii ssp. timopheevii genotypes showed significantly higher concentration of grain Fe and Zn than CS and LDN. Aboundant genetic variability of both the Fe and Zn concentrations was observed among the T. timopheevii ssp. timopheevii accessions, averagely varied from 47.06 to 90.26 mg kg−1 and from 30.05 to 65.91 mg kg−1, respectively. Their grain Fe and Zn concentrations between years exhibited a significantly positive correlation with the correlation coefficients r = 0.895 and r = 0.891, respectively, indicating the highly genetic stability. Flag leaf possessed twice or three times higher concentrations for both Fe and Zn than grain, and a significantly high positive correlation appeared between the two organs with r = 0.648 for Fe and r = 0.957 for Zn concentrations, respectively, suggesting flag leaves might be indirectly used for evaluating grain Zn and Fe contents. Significant correlations occurred between grain Fe and Zn concentrations, and between grain Zn concentration and the two agronomic traits of plant height and number of spikelets per spike. Both the concentrations were not related to seed size or weight as well as NAM-G1 gene, implying the higher grain Fe and Zn concentrations of T. timopheevii ssp. timopheevii species are not ascribed to concentration effects of seed and the genetic control of NAM-G1 gene. There might be some other biological factors impacting the grain’s Zn and Fe concentrations. These results indicated T. timopheevii ssp. timopheevii species might be a promising genetic resource with high Fe and Zn concentrations for the biofortification of current wheat cultivars.