The utility of explicit spatial predictions for biodiversity assessment is investigated with New Zealand fern flora. Distributions of 43 species were modelled from climatic and landform variables and predicted across New Zealand using generalised additive models (GAM). An original package of functions called generalised regression analysis and spatial prediction ( GRASP) was developed to perform the analyses. On average, for the 43 models, the contributions of environmental variables indicate that mean annual temperature is the most important factor at this broad regional scale. Both annual solar radiation and its seasonality had higher correlations than temperature seasonality. Measures of water availability such as ratio of rainfall to potential evapotranspiration, air saturation deficit and soil water deficit presented significant contributions. Lithology was a better predictor than slope and drainage. These results are similar to those obtained from analyses of the distributions of New Zealand tree species and are consistent with the hypothesis that both tree and fern diversity are highest on sites conducive to high productivity. In order to identify hotspots of fern diversity, spatial predictions of individual species were summed up. The resulting map gave a very similar result to the direct prediction of their corresponding richness ( number of species by plot out of 43 spp.). As a consequence, and where individual species models were not all available, the number of species within different species assemblages was directly modelled. Predicted richness hotspots of total species ( out of 122 spp.), selected species ( out of 43 and 21 spp.) and common species ( out of 23 spp.) present very similar spatial patterns and are highly correlated. Richness of uncommon species ( out of 39 spp.) was also accurately predicted, but presented a different spatial pattern. The number of rare species ( out of 60 spp.) was not correctly modelled. Even though the lack of data for rare species clearly limits the application of this approach, fern community composition of more common species can be partially reconstructed from individual species predictions. This case study offers therefore a consistent approach not only for biodiversity hotspots identification, but also for setting targets to biodiversity assessment and restoration programs.