The ambient atmosphere is dominated with pollen and spores, which trigger allergic reactions and diseases and impact negatively on human health. A survey of pollen and fungal spores constituents of the atmosphere of Garki, Abuja (North-Central Nigeria) was carried out for 1 year (June 1, 2011–May 31, 2012). The aim of the study was to determine the prevalence and abundance of pollen and fungal spores in the atmosphere and their relationship with meteorological parameters. Airborne samples were trapped using modified Tauber-like pollen trap, and the recipient solutions were subjected to acetolysis. Results revealed the abundance of fungal spores, pollen, fern spores, algal cysts and diatoms in decreasing order of dominance. The atmosphere was qualitatively and quantitatively dominated by pollen during the period of late rainy/harmattan season than the rainy season. Numerous fungal spores were trapped throughout the sampling periods among which Alternaria spp., Fusarium spp., Cladosporium spp. and Curvularia spp. dominated. These fungi have been implicated in allergic diseases and are dermatophytic, causing diverse skin diseases. Other pathogenic fungi found in the studied aeroflora were Dreschlera spp., Helminthosporium spp., Torula spp., Pithomyces spp., Tetraploa spp., Nigrospora ssp., Spadicoides spp., Puccinia spp. and Erysiphe graminis. Total pollen and fungal spores counts do not show significant correlation with meteorological parameters.