Common root rot, caused by Cochliobolus sativus (Ito and Kurib) Drechs. ex Dastur, is a major soil-borne disease of spring and winter wheat (Triticum aestivum L. em Thell.) on the Canadian prairies. Resistance to common root rot from Thinopyrum ponticum (Podp.) Liu and Wang was transferred into wheat via crossing with Agrotana, a resistant wheat - Th. ponticum partial amphiploid line. Evaluation of common root rot reactions showed that selected advanced lines with blue kernel color derived from a wheat x Agrotana cross expressed more resistance than the susceptible T. aestivum 'Chinese Spring' parent and other susceptible wheat check cultivars. Cytological examination revealed 41 to 44 chromosomes in the advanced lines. Genomic in situ hybridization, using total genomic DNA from Pseudoroegneria strigosa (M. Bieb) A. Löve (St genome) as a probe, demonstrated that the blue kernel plants had two pairs of spontaneously translocated J-Js and Js-J chromosomes derived from the J and Js genome of Th. ponticum. The presence of these translocated chromosomes was associated with increased resistance of wheat to common root rot. The lines with blue aleurone color always had a subcentromeric Js-J translocated chromosome. The subtelocentric J-Js translocated chromosome was not responsible for the blue kernel color. The genomic in situ hybridization analysis on meiosis revealed that the two spontaneous translocations were not reciprocal translocations.