The introduction of alien ungulates is a major threat for the survival of endangered plants, especially in island ecosystems. However, very few studies have investigated the potential damage of large herbivores on plant diversity in Mediterranean protected areas. In this study, we describe the population structure and the long-term dynamics of the main populations of the Sardinian narrow endemic Centaurea horrida Bad. (Asteraceae), by means of permanent plots where individual plants were tagged and monitored through 6 years (2004-2009). We monitored this endangered plant at three sites: two were protected areas where introduced and feral ungulates are present, and the other one was a non-protected site without introduced ungulates. We found that adults and saplings were more abundant at the non-protected site. Through matrix models, we also highlighted that the non-protected population showed the highest population growth rate. Finally, by means of an exclusion experiment for ungulates at one protected site, we demonstrated that herbivores had a negative effect on the survival of seedlings and adult plants, and reduced the stochastic population growth rate. An LTRE analysis showed that differences in the survival, especially of adult individuals, had the highest responsibility in explaining the higher population growth rate when herbivores are excluded. Our study constitutes a clear example on how the protection of alien large herbivores can have opposite effects on the conservation of an endangered plant. Some management options are proposed, and the urgent need of manipulative experiments on species-specific interactions between protected plants and alien herbivore species is invoked.