Aegilops comosa (MM, 2n = 2x = 14), an important diploid species belonging to wheat tertiary gene pools, contains many excellent genes/traits, including disease resistance for wheat breeding. In this study, three sister lines, NAL-32, NAL-33, and NAL-34, were identified from a wheat - Ae. comosa distant cross using fluorescence in situ hybridization (FISH) combined with single nucleotide polymorphism (SNP) microarray analysis. Genetically, NAL-32 contained neither an alien nor translocation chromosome, whereas NAL-33 and NAL-34 had disomic 7M/7A substitution chromosomes but differed in the absence (NAL-33) or presence (NAL-34) of 1BL/1RS translocation chromosomes. The substitution of 7M/7A in NAL-33 and NAL-34 was verified using wheat 55 K SNP arrays but 1BL/1RS translocation in NAL-34 was not. The two 7M/7A substitution lines, NAL-33 and NAL-34, had similar stripe rust resistance, and both showed higher stripe rust resistance than NAL-32 and their parents, suggesting that stripe rust resistance in NAL-33 and NAL-34 was derived from the 7M of Ae. comosa and that their resistance was likely irrelevant to 1BL/1RS translocation. Meanwhile, the three NAL lines also showed higher grain weights (grams per 50 grains) than one to three of their three wheat parents, and the two 7M/7A substitution lines, NAL-33 and NAL-34, had larger seed size-related traits than NAL-32, suggesting that both the 7M and 1BL/1RS chromosomes had positive effects on seed size-related traits. The results provide important bridge materials that can potentially be used for transferring stripe rust resistance, as well as seed size-related traits from Ae. comosa to wheat.