Background The increasing number of aerobiological stations empower comparative studies to determine the relationship between pollen concentrations in different localities and the appropriate distance, which should be established between sampling stations. In Qatar, this is basically the first aerobiological study for a continuous monitoring interval. Objectives The study aimed to assess the abundance and seasonality of the most prevalent pollen types, plus identify potential differences between two sites within the country. Methods Airborne pollen data were collected during 2017–2020 by using Hirst-type volumetric samplers in Doha capital city and Al Khor city in Qatar, placed 50 km apart. Results Higher total pollen indexes were recorded in the Al Khor station (2931 pollen * day/m³) compared to the Doha station (1618 pollen * day/m³). Comparing the pollen spectrum between the sampling stations revealed that ten pollen types were found in common. Amaranthaceae and Poaceae airborne pollen constituted 73.5% and 70.9% of the total amount of pollen detected at the samplers of Al Khor station and Doha station. In both sampling sites, a very pronounced seasonality was shown; August–October appeared as the period with the most intense incidence of atmospheric herbaceous pollen, with 71% and 51% of the annual total counts in Al Khor and Doha stations, respectively. August (Al Khor, 21%; Doha, 9%), September (Al Khor, 33%; Doha, 26%), October (Al Khor, 17%; Doha, 16%) were the months in which the herbs pollen concentrations were highest. Significant statistical differences between the two stations were observed in specific pollen types with local distribution in each trap’s vicinity. Conclusions Comparison of data obtained by the two samplers running at a distance of 50 Km indicated that potential inter-site differences could be attributed to the vegetation surrounding the city having a decisive influence on data collected.