Urbanisation has strong effects on biodiversity patterns, but impacts vary among species groups and across spatial scales. From a local biodiversity management perspective, a more general understanding of species richness across taxonomic groups is required. This study aims to investigate how fine-scale land-cover variables influence species richness patterns of locally threatened and alien species. The study was performed in Trondheim, Norway, covering a steep urbanisation gradient. Spatially correlated Generalised Linear Mixed Effects Models predicting the number of all-, threatened-and alien species by taxon, habitat, habitat heterogeneity and mean aspect within 500 m×500 m grid cells were constructed. The habitat categories were based on detailed land-cover maps. The highest number of threatened species was found in habitats relatively less affected by humans, whereas the number of alien species were only dependent on taxonomic group and spatial correlation. It is shown that land-cover variables within an administrative border can be used to make predictions on species richness within overarching species groups. Recommendations to biodiversity management agencies are to ensure protection of natural habitats to favour locally threatened species, and closely monitor urban areas to mitigate the introduction and spread of alien species.