Hybridization and introgression via interspecific gene flow are common processes in the plant kingdom. The effectiveness of these processes is governed by the strengths of multiple zygotic barriers. These barriers have often been quantified in artificial settings using laborious and time-consuming hand-pollination experiments, but their quantification is nonexistent at the landscape level. In this study, we utilized gene flow data within a spatially explicit simulation to assess the strengths of zygotic barriers. Our model system consisted of Populusnigra and its hybrid, P.×canadensis, which interbreed under natural conditions. The study population was located in the floodplain of the Eder River in Central Germany. Pollen-mediated introgression rates from hybrid males into the seeds of individual female trees were used as the target pattern using an inverse modeling approach. Simulations that treated pollen from both taxa equally revealed a large discrepancy between the observed and modeled rates of introgression for both taxa. The discrepancy was reduced by introducing a zygotic barrier against the pollen from the hybrid males. The best model outcome indicated comparably strong zygotic barriers acting against pollen-mediated introgressive gene flow into the two parental taxa, P.nigra and P.×canadensis. The sensitivity of our model was tested by applying different dispersal functions. Four common probability density functions were used along with a pollen dispersal function that had previously been fitted to gene flow data from the same dataset. The best barrier value was almost independent of the dispersal functions used here. Moreover, it was within the range previously determined in hand-pollination-based investigations, validating our model. These data indicate that the inverse modeling approach is a powerful method for quantifying hidden processes, and we discuss its use as a valuable tool for generating new insights into plant mating systems that are relevant to evolutionary biology and risk analysis in conservation efforts