Newly synthesized wheat-rye allopolyploids were investigated by genomic in situ hybridization, over the first, second, third and fourth allopolyploid generations. Inter and intra chromosome connections were observed in 12 root-tip cells of CA4.4.7 (S(2) generation), and translocations between wheat and rye chromosomes were also detected in five root-tip cells. In root-tip cells of CA4.4.7.5 and CA4.4.7.2.2 (S(3) and S(4) generation), the chromosome connections occurred again, a dissociative small rye segment was detected in seven cells of CA4.4.7.5. In plants MSV6.1 and MSV6.5 (S(1) generation), almost half of the root-tip cells contained 13 rye chromosomes and the rest held 12 rye chromosomes, and all the cells of the two plants contained 42 wheat chromosomes. Five pairing configurations of rye chromosomes, including 5 II + 3 I, 6 II + 1 I, 6 II, 5 II + 2 I and 4 II + 4 I, were observed in pollen mother cells of the two plants. The two plants' progeny, including S(2), S(3), and S(4) generation plants, contained 42 wheat chromosomes and 12 rye chromosomes. Therefore, the inter chromosome translocation and unequal chromosome division could occur in somatic cells of wide hybrids. The unequal chromosome division in somatic cell could induce chromosome elimination at the early stages of allopolyploidization.