Wheat alloplasmic lines are plants where the cytoplasmic genome of one wheat species was substituted by those of a wild relative, while maintaining the original nucleus. Our project studied differential responses of various alien cytoplasm in a specific nuclear background to various pathogens to identify NC interaction effects on biotic stress tolerance. This study analyzed fifty selected alloplasmic lines that were tested for disease response to Pyrenophora tritici-repentis isolates Br15 and Pti2. Results indicate that Ae. bicornis cytoplasm with nuclei donor of Chris and Selkirk provides increased resistance to tan spot isolate Br15. Puccinia triticina was used in determining differential responses between alloplasmic and euplasmic lines. A bulk set of four leaf rust isolates indicated Aegilops heldreichii cytoplasm with Chris nucleus provides resistance to the susceptible euplasmic line Chris and showed increased resistance to both tan spot isolates. These data indicates that cytoplasmic variability can improve resistance to plant diseases.