A combination of meiotic pairing analysis and in situ hybridization (genomic in situ hybridization [GISH], multicolor GISH [mcGISH] and fluorescence in situ hybridization [FISH]) of five Triticum aestivum (Linnaeus, 1753) - Elytrigia elongata (Podpěra, 1902) (2n = 10x = 70) amphiploids was employed to investigate the genomic constitution and relationships between wheat and alien chromosomes. GISH, multicolor GISH and FISH patterns of mitotic chromosomes indicate that the genomic constitution of the five partial amphiploids (XY693, XY7430, SN19, SN20 and SN122) are 14A + 12B + 14D + 8Js + 8J, 12A + 16B + 14D + 2St + 8Js + 2J + 2 W-E, 14A + 14B + 14D + 4St + 8Js, 14A + 14B + 14D + 2St + 10Js + 2J, and 14A + 14B + 14D + 2St + 8Js + 4J, respectively. Analysis of meiotic chromosome pairing in the F1 hybrids between these five partial amphiploids suggests that SN20 and SN122 are the most closely related amphiploids and are somewhat related with XY693 and XY7430. However, the alien chromosome constitutions of SN19 differed from the other four amphiploids. In addition, a new pairing between wheat and E. elongata chromosomes was distinguished in some cells of the hybrids SN19 × XY7430, SN20 × XY7430 and SN122 × XY7430.