Wild and cultivated relatives of wheat are an important source of genetic factors for improving the mineral composition of wheat. In this work, a wheat panel consisting of modern bread wheat varieties, landraces, and introgression lines with genetic material of the wheat species Triticum timopheevii, T. durum, T. dicoccum, and T. dicoccoides and the synthetic line T. kiharae was used to identify loci associated with the grain zinc (GZnC) and iron (GFeC) content. Using a BLINK model, we identified 31 and 73 marker–trait associations (MTAs) for GZnC and GFeC, respectively, of which 19 were novel. Twelve MTAs distributed on chromosomes 1B, 2A, 2B, 5A, and 5B were significantly associated with GZnC, five MTAs on 2A, 2B, and 5D chromosomes were significantly associated with GFeC, and two SNPs located on 2A and 2B were related to the grain concentration of both trace elements. Meanwhile, most of these MTAs were inherited from At and G genomes of T. timopheevii and T. kiharae and positively affected GZnC and GFeC. Eight genes related to iron or zinc transporters, representing diverse gene families, were proposed as the best candidates. Our findings provide an understanding of the genetic basis of grain Zn and Fe accumulation in species of the Timopheevi group and could help in selecting new genotypes containing valuable loci.