OBJECTIVE Aeroallergens are airborne organic substances which are responsible for allergenic diseases in hypersensitive individuals. People are exposed to their allergens either directly or after their entrance into the interiors. The spatio-temporal pattern of aeroallergens and their relationship with weather variability in Abuja and Nassarawa, North-Central Nigeria was studied. METHODS Aerosamples were trapped with modified Tauber-like pollen traps. Samples were collected monthly and centrifuged at 2500rpm for 5 min and subjected to acetolysis. Meteorological data were collected from the Nigerian Meteorological Agency. CONCLUSIONS Aeroallergens concentration were unequivocally regulated by weather variables in both locations, indicating the possible use of aeroallergens especially pollen and spores as bio-indicators of weather variations and change. Aeroallergens encountered were fungal spores, pollen, diatom frustules, fern spores, algal cyst/cells in decreasing order of dominance. Among pollen group, Poaceae, Amarathaceae/Chenopodiaceae and Hymenocardia acida dominated. Spores of Smut species, Puccinia, Curvularia and Nigrospora were major contributors among aeromycoflora. Fungal spores morphotype dominated during the rainier months and were major contributors of the aeroallergen spectrum with those belonging to Deuteromycete preponderant. Aeroallergens which were previously identified as triggers of conjunctivitis, asthma, allergic sinusitis and bronchopulmonary allergic diseases were frequently present in both locations. Pollen prevailed more during the harmattan, influenced by northeast trade wind. Pollen component differed and was based on autochthonous source plants, indicating difference in sub-vegetational types.