The spontaneous flow of genes from wheat to jointed goatgrass is of great concern to breeders intending to release herbicide-resistant wheat. The objectives of this research were to study how genes could flow from wheat to jointed goatgrass through crossing and backcrossing between these two species and, based on this knowledge, to propose possible ways to minimize the chance of gene flow between them. Results showed that the wheat × jointed goatgrass hybrid can only serve as a female parent to produce the BC1 generation. The BC1 generation was found to have 1.8% male fertility and 4.4% female fertility, indicating that it could serve as either the male or female parent to produce a BC2 generation. The fertility of the resultant BC2 generation further increased. The average male, female, and self-fertility was 8.9, 18.0, and 6.9%, respectively. After the BC2 generation, the backcross progeny has three possible ways to reproduce: to pollinate jointed goatgrass, to be pollinated by jointed goatgrass, or to pollinate itself. Restoration of the chromosome number of jointed goatgrass continues as the BC2 generation is selfed, but some plants can contain an alien chromosome over generations. The possible ways to reduce the chance of gene flow between these two species are (1) prevent the production of hybrids, (2) prevent the production of the BC1 generation, and (3) put a herbicide-resistant gene on the A- or B-genome of wheat.