Distant hybridization is a practical way to introduce the chromatins conferring agronomically desirable genes of the wheat related species into the common wheat in order to enhance the diversity of the wheat genetic pool. The aim of this study was to identify the homozygous small segmental translocation lines with excellent agronomic performances among the progenies of the hybridization between wheat and alien species by using Genomic In Situ Hybridization (GISH) as the cytogenetic tool. In this study, the translocation progenies of the hybridization between the wheat-Agropyrum cristatum disomic substitution line 4844-8 and common wheat or between the disomic addition line 4844-12 and common wheat were studied as the research materials. Two intercalary translocation lines with a pair of small homozygous A. cristatum chromatin segments respectively were identified with GISH. One intercalary line(104-3) was resistant to powdery mildew and was with high thousand grain weight(TGW). The other intercalary line(19-2) was excellent for its high grain number per spike(GNPS) and high TGW. The excellent agronomic performances of these 2 lines indicated that they were both elite genetic resources, which could be used in the future to broaden the wheat genetic basis.