Twenty three aerophytic blue-green algal species were isolated and identified from 5 districts in Cairo, namely: Nasr City, Abassiya, Downtown, Maadi and Tebbin. Downtown contained the highest numbers of total algal species (13 species) during the study throughout the years 2004-2005 in comparison to other districts. The composition of aeroalgal taxa varied with seasonal changes. Chroococcus limenticus, Lyngbya lagerheimii, Phormidium ambigum and Schizothrix purpurascens have been isolated during the both years 2004-2005, while the rest of algal species (nineteen species) have been trapped either in 2004 or 2005. Nostoc spp. is the most common isolate of all algal isolates during the study. Analysis of air pollutants such as SO2, NO2, suspended particles less than 10 micro (PM10), black smoke and lead are also recorded. Downtown showed the highest concentration of SO2, NO2 and PM10 level during the present study in comparison to other sites. The interaction between air pollutants and aerophytic Cyanophyceae species was concerned.