Moss spores are present in aerobiological samples, but their low representation, lack of known allergenic properties, and difficult identification have led to their being overlooked by aerobiologists so far. The data about their presence in the atmosphere and the factors that influence them are, however, important from the biodiversity conservation point of view, since they give us information about their ability to spread to new habitats. In this pilot study, we analysed their presence in the atmosphere of Bratislava city, Slovakia (2018–2023), using Burkard volumetric sampler, and determined the most significant factors influencing its temporal distribution. The size category of 13–18 µm was the most represented in the samples. Environmental factors influenced the daily spore concentrations and the characteristics of the whole spore season. The start of the Main Spore Season (MSS) depended mainly on the temperatures in November–January, initiating earlier growth of sporophytes in the following year, while the intensity of the MSS was influenced by high humidity in April, stimulating the formation of spores in sporangia. The daily concentration of airborne moss spores was mostly influenced by the actual temperature and wind speed, promoting the release and dispersal of spores, and precipitation lowering their levels due to the “wash-out” effect, although no intradiurnal pattern was observed. More data from other locations is needed to determine the role of atmospheric spore transport for the conservation of moss species facing anthropogenic climatic change.