Alternariais a plant pathogen and human allergen.Alternaria alternatais one of the most abundant fungal spores in the air. The purpose of this study was to examine whetherAlternariaspp.spore concentrations can be used to predict the abundance and spatio-temporal pattern ofA.alternataspores in the air. This was investigated by testing the hypothesis thatA.alternatadominates airborneAlternariaspp. spores and varies spatio-temporally. Secondarily, we aimed at investigating the relationship between airborneAlternariaspp. spores and the DNA profile ofA.alternataspores between two proximate (~ 7 km apart) sites. These were examined by samplingAlternariaspp. spores using Burkard 7-day and cyclone samplers for the period 2016–2018 at Worcester and Lakeside campuses of the University of Worcester, UK. DailyAlternariaspp. spores from the Burkard traps were identified using optical microscopy whilstA.alternatafrom the cyclone samples was detected and quantified using quantitative polymerase chain reaction (qPCR). The results showed that eitherA.alternataor otherAlternariaspecies spores dominate the airborneAlternariaspore concentrations, generally depending on weather conditions. Furthermore, althoughAlternariaspp. spore concentrations were similar for the two proximate sites,A.alternataspore concentrations significantly varied for those sites and it is highly likely that the airborne samples contained large amounts of small fragments ofA.alternata. Overall, the study shows that there is a higher abundance of airborneAlternariaallergen than reported by aerobiological networks and the majority is likely to be from spore and hyphal fragments.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00484-023-02480-w.