Grafting is a common method for clonal propagation of fruit trees. Moreover, it serves as a mean to deal with abiotic stress, adjust tree growth vigor, increase yield, and improve other fruit quality traits. Investigations of rootstock and scion graft relationships have originally focused on anatomical and cellular development, nutrient transport, and hormonal movement across graft union. Discovery of long distance transport of mRNA and small RNAs in phloem tissues of rootstock and scion has provided new opportunities for investigation. In this study, we report on the endogenous transport of Gibberellic acid insensitive (GAI) across graft union of a traditional local Chinese pear cultivar, Pyrus bretschneideri cv. Yali (scion), and a wild Pyrus betulaefolia cv. Bunge (rootstock). Cleaved amplified polymorphic sequence analysis RT-PCR indicated that Pyrus-GAI can be transported within 4 and 10 days after micro-grafting, and it can also be transported to a 10–50-cm tall scion of a 2-year-old grafting tree. To further investigate the transport capacity of Pyrus-GAI transcript, a 35S:pear (P. betulaefolia)-GAI transgenic tobacco (Nicotiana tabacum L. cv. Samson.) was prepared and grafted to wild-type tobacco. RT-PCR indicated that sustained transmission of GAI mRNA through the graft union occurred from the 15th day after grafting. The results have laid a foundation for improving rootstock and regulating the properties of scion in fruit trees by transgenic technology.