Crop-to-wild gene flow can reduce the fitness and genetic integrity of wild species. Malus sylvestris, the European crabapple fruit tree, in particular is threatened by the disappearance of its habitat and by gene flow from its domesticated relative, Malus domestica. With the aims of evaluating threats for M. sylvestris and of formulating recommendations for its conservation, we studied here, using microsatellite markers and growth experiments: i) hybridization rates in seeds and trees from a French forest and in seeds used for replanting crabapples in agrosystems and in forests, ii) the impact of the level of M. domestica ancestry on individual fitness tree, and iii) pollen dispersal abilities in relationship with crop-to-wild gene flow. We found substantial contemporary crop-to-wild gene flow in crabapple tree populations and superior fitness of hybrids compared to wild seeds and seedlings. Using paternity analyses, we showed that pollen dispersal could occur up to 4 km and decreased with tree density. The seed network furnishing the wild apple reintroduction agroforestry programs was found to suffer from poor genetic diversity, introgressions, and species misidentification. Overall, our findings indicate supported threats for the European wild apple steering us to provide precise recommendations for its conservation.