Based on the chromosome origin identification of an Agropyron intermedium chromosome with BYDV resistance in Yi4212, a BYDV-resistant substitution line derived from the hybrids between 77-5433 and Zhong5, its ability compensating the lost wheat chromosomes and its transmission rate were investigated. The results indicated that the BYDV-resistant chromosomes originated from Zhong 5 could compensate the wheat chromosomes of homotologous group 2, 5 and 7. The chromosome conferring resistance to BYDV showed the intendance to substitute 2D rather than 2A, 2B wheat chromosomes in disomic substitution lines. In (77-5433/Zhong 5) selfing F2 population, 10 kinds of chromosome constitutions, including 9 expected and 1 unexpected kinds, and much chromosome number variation and little chromosome structure variation were observed. The transmission rate of the BYDV-resistant chromosome and the gametes carrying this chromosome were 56.3% and 33.0% respectively, both are lower than the expected ratio 75.0% and 50.0%. Some reasons were given to explain the related results, and chromosome in situ hybridization was an efficient and accurate way in studying the alien chromosome behavior in wheat background.