The potential for gene flow between crops and their wild relatives is now well established. However, few studies have investigated the effects of crop genes on fitness in natural populations, or the indirect ecological consequences of their naturalisation. This study investigates the likelihood of genes derived from North American gooseberry species (which are resistant to the coevolved American gooseberry mildew) becoming established in mildew-susceptible native British gooseberries, and the impact of this on their invertebrate herbivores. The results reveal that seedlings containing resistance genes had significantly higher survival rates than susceptible native plants. Alien genes were more likely to establish when introgressed into native genomes and when crossed with local provenance genotypes. Furthermore, plants containing alien genes tended to support significantly more but smaller invertebrates. Thus, the potential ecological effects of crop gene escape may vary with source and recipient genome and such effects may not be directly related to the gene’s function.