Alien species are considered a major driver of extinction risk. Preventing high-impact aliens from being introduced is more necessary than ever to mitigate the current biodiversity crisis. Invasive species risk assessments look at the characteristics of potential invaders but rarely consider how different they are from the native residents that they might threaten. Therefore, we tested whether the impacts of an alien species on a native species can be predicted using the pairwise phylogenetic distance (PPD) between them. Specifically, we analysed whether the PPD of 1407 pairs of native–invasive alien plants is related to the extinction risk of the native plants. We showed that natives threatened by close alien relatives have a significantly higher extinction risk, especially on oceanic islands. This finding argues for consideration of PPD, or at least the presence of congeneric or confamilial native species, in risk assessment of potential impacts of newly introduced alien species and priorization of management of already naturalized alien species.