From clinical point of view, knowledge of the pollen season and loads in the atmosphere of every community is important so as to guide on incidence and management of pollinosis. The aim of this work therefore is to evaluate the weekly constituents of the atmospheric pollen and fern spores of two communities in Lagos Nigeria and the relationship, if any, between the weekly aeroflora and hospital reported pollinosis cases. As part of efforts to contribute to the gathering of aerobiological data in Lagos State, a weekly gravimetric sampling of two locations (Ipaja and Ogba) in Lagos, Nigeria were undertaken from January 2018â€“December 2018 and the reported pollinosis cases (asthma and rhinitis) were collected from the surrounding hospitals. The samplers were placed on rigid platforms at 2Â m above the ground level, the harvested residues were subjected to standard palynological procedure and twenty microlitres of each sample were studied microscopically. A total of 30 pollen taxa were identified with Amaranthaceae (544) dominating the palynomorphs at Ipaja and Elaeis guineensis (347) at Ogba. Using correlation (r = 0.1, p-value = 0.55 at Ipaja while r = 0.3, p-value = 0.33 at Ogba) and RDA test at p > 0.05, there is insignificant positive relationship between pollinosis cases and abundance of palynomorphs. However, at Ipaja, RDA indicated Poaceae and Elaeis guineensis as the possible drivers for asthma cases while Amaranthaceae and fungal spores were identified as weak drivers for catarrh. At Ogba, the loess curve and correlation test showed a significant positive relationship at p < 0.05 between the reported pollinosis cases and abundance of recovered palynomorph. Elaeis guineensis, Nephrolepis sp. and Dryopteris sp. seem to be the main drivers of asthma while Casuarina sp. and fungal spores perhaps drove catarrh. Dryopteris and Nephrolepis spores are firstly implicated as possible allergenic aeroconstituents in Nigeria in this work. The results from this work provide a background reference for the general public and hypersensitive individuals on the spatial distribution of pollen grains and fern spores in the study areas of Lagos as well as being a guide to the identification of culprit allergenic aeroconstituent.