The exploration of factors and processes affecting biodiversity loss is central to nature management and wildlife conservation, but only recently has knowledge about the absence of species been recognized as a valuable asset to understand the current biodiversity crisis. In this paper, we explore the dark diversity (species that belong to a site-specific species pool but that are not locally present) of breeding birds in Denmark assessed through species co-occurrence patterns. We apply a nation-wide atlas survey of breeding birds (with a 5 × 5 km resolution), to investigate how landscape characteristics may influence avian diversity, and whether threatened and near threatened species are more likely to occur in dark diversity than least concern (LC) species. On average, the dark diversity constituted 41% of all species belonging to the site-specific species pools and threatened and near-threatened species had a higher probability of belonging to the dark diversity than least concern species. Habitat heterogeneity was negatively related to dark diversity and the proportional cover of intensive agriculture positively related, implying that homogeneous landscapes dominated by agricultural interests led to more absent avian species. Finally, we found significant effects of human disturbance and distance to the coast, indicating that more breeding bird species were missing when human disturbance was high and in near-coastal areas. Our study provides the first attempt to investigate dark diversity among birds and highlights how important landscape characteristics may shape breeding bird diversity and reveal areas of considerable species impoverishment.