Jointed goatgrass is an important weed of wheat in the United States and other parts of the world. Under field conditions, wheat and jointed goatgrass can hybridize and produce backcross derivatives, a situation that may allow gene flow between these two species. In order to gain a better understanding of the factors governing gene flow, a study to characterize patterns of mating between these two species was undertaken. Chloroplast and nuclear microsatellite markers were used to evaluate the parentage of 413 first-generation backcross (BC1) seeds obtained from 127 wheat–jointed goatgrass F1 hybrids, produced naturally under field conditions. Of the 127 hybrids evaluated, 109 (85.8%) had jointed goatgrass as the female parent, whereas the remaining 18 F1 plants (14.2%) had wheat as the female parent. Of the 413 BC1 plants analyzed, 358 (86.7%) had wheat and 24 (5.8%) had jointed goatgrass as the male backcross parent. The male parentage of 31 BC1 (7.5%) plants could not be determined. Under natural field conditions, wheat was the prevalent pollen donor for the production of hybrids and first-generation backcross derivatives. However, hybrids and backcrosses with jointed goatgrass as the male parent also were observed. Thus, the establishment and persistence of a zone of hybridization between these species would result in the development of jointed goatgrass carrying wheat genes.