The concept of altered phenotypes in plants with alien cytoplasms has been known ever since Mendel's Laws of Inheritance were re-discovered. However, knowledge is still lacking on the genetic basis of these differences. A species-cytoplasm specific (scs) gene, derived from the nuclear genome of Triticum timpheevii, improved nuclear-cytoplasmic (NC) and embryo-endosperm compatibility in alloplasmic durum wheat (T. turgidum) with T. longissimum cytoplasm, but this line was male sterile. A vitality gene (Vi) restored male fertility and seed viability. In the absence of Vi, plants with scs have normal vigor, are male sterile, and produce a 1:1 ratio of viable and aborted seed. In the absence of scs plants with the Vi are weak, but fertile. In the absence of both scs and Vi, the T. turgidum nucleus is incompatible with T. longissimum cytoplasm. Two populations segregating for scs and Vi were produced in order to i) determine the chromosomal locations of scs and Vi; ii) identify DNA markers; and iii) determine the interactions between the two genes. From the analysis of 166 individuals segregating for presence/absence of scs as indicated by plant vigor, and polymorphic RFLP clones, we have located scs on chromosome 1AL in addition, we have located Vi to 1BS using RFLP markers on 123 individuals. All recombinants between Vi and its closest RFLP marker are of one type, i.e. having the marker, but lacking expression of Vi. This indicates that other nuclear genes may be inhibiting the expression of Vi. We were able to map markers for scs in the population developed to study Vi, and vice versa, because both genes were segregating in both populations. The presence of DNA markers for these genes allowed us to determine the allelic state of each gene and identify possible interactions. In one population there was an additive effect on self fertility with Individuals having one copy of scs and two copies of Vi having the most fertility. In the other population, there was no effect on self-fertility of one versus two copies of scs in the presence of one copy of Vi.