Determining the efficacy of using indicator species to predict the spatial location of biodiversity hotspots is one way of maximising the conservation of biodiversity in already threatened habitats. Recent evidence from Europe suggests raptors can play such an indicator role, so we tested this approach with a globally threatened southern hemisphere species, the Black Harrier Circus maurus. We asked if this species, found in South Africa’s mega-diverse Cape Floral Kingdom, breeds in habitat fragments that were more diverse in terms of small mammals, birds and plants than unoccupied fragments of similar size. Renosterveld is a highly fragmented habitat that has lost > 90% of its original extent and remains only on privately-owned lands. Surveys of small mammals, birds and plants undertaken in 20 fragments in the Overberg region, South Africa, revealed nine with breeding harriers and 11 without harriers. Harrier-occupied fragments were associated with a 3.5 fold higher number of bird species and higher small mammal species richness than unoccupied ones. There was a lower abundance of most plants in occupied patches, except for red grass Themeda triandra which is an indicator of pristine renosterveld. Vegetation structure was significantly different, with harriers nesting on patches with taller, more open vegetation. While the diversity trends were not statistically significant, a positive trend between the presence of harriers and higher abundance of red grass – as an indicator of the more pristine state of the patch, suggests that harriers might allow biodiversity managers a heuristic approach for selecting the remaining patches of pristine renosterveld. The need for intensive sampling of several taxa leads to small samples and a lack of clear-cut trends for these top predators as indicators of plant diversity.