We examine the role of ecological interactions on effective gene flow from genetically manipulated plants to their wild relatives. We do so by constructing and applying to oilseed rape (OSR) an analytical model for interaction between plants with and without an insect resistance (IR) allele in natural communities, incorporating documented levels of herbivore variability. We find that with reasonable values of advantage to the IR allele, little concomitant disadvantage (physiological costs of the allele) restricts it to low proportions of the natural population for large numbers of generations. We conclude that OSR IR transgenes are unlikely to pose an immediate threat to natural communities. Our model identifies those factors best able to regulate particular transgenes at the population level, the most effective being impaired viability of seeds in the period between production and the following growing season, although other possibilities exist. Because solutions rely on ratios, limiting values of regulating factors are testable under controlled conditions, minimizing risk of release into the environment and offering significant advancement on existing testing programmes. Our model addresses folivory but is easily modified for herbivory damaging the seed or directly affecting seed production by infested plants, or for pathogens altering seed survival in the seedbank.