Anthropogenic impact and loss of genetic diversity threaten more than 50% of raptors. These threats are particularly pronounced for island- endemic species, which occupy small areas, making them more vulnerable to rapid environmental changes. The Reunion harrier (Circus maillardi) is a typical example of the challenges encountered by island- endemic species. In this study, we characterize genetic variation at near-neutral and coding loci to test the historical impact of human activity on harrier populations, and evaluate their (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants, but is unlikely to have allowed the purging of mildly deleterious variants. Our study provides an example of the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.