Triticum longissimum cytoplasm is incompatible with the T. turgidum nuclear genome. Two nuclear genes, scs and Vi, derived from the nuclear genome of T. timopheevii and by a spontaneous mutation, respectively, restore nuclear-cytoplasmic compatibility, normal plant vigor, and male fertility in these alloplasmic genotypes. The objectives of this study were (i) to determine the chromosomal locations of scs and Vi; (ii) to identify DNA markers for scs and Vi; and (iii) to determine the interactions involving the dosage of scs and Vi. Two populations segregating for scs and Vi were produced and scored for seedling vigor (indicating presence of scs) and degree of self-fertility (indicating presence of Vi). Four RFLP markers were mapped near scs. Aneuploid analysis revealed that these markers, and hence the scs gene, are located on the long arm of chromosome 1A. Four RFLP markers were mapped near Vi on 1BS. Results indicated that other factors may be inhibiting the expression of Vi. We determined the dosage of scs and Vi in both populations with the aid of the linked RFLP markers. Individuals with two versus one dose of scs had reduced self-fertility, while individuals with two versus one dose of Vi had similar self-fertility.