Five aquatic sites of National Botanical Garden of Iran monthly were sampled from December 2003 to November 2004. Total number of 68 genera in 18 families and 11 orders of the planktonic Diatoms were identified. Among the families Bacillariaceae with 19 genera and species showed the highest species richness. Cymbellaceae (11 species), Naviculaceae (7 species), Surirellaceae (6 species), Pleurosigmataceae (4 species), Fragilariaceae and Achnanthaceae each with 4 species, Pinnulariaceae and Gomphonemaceae each with 2 species and Rhopalodiaceae, Cosmioneidaceae, Diadesmidiaceae, Amphipleuraceae, Catenulaceae, Melosiraceae, Mastogloiaceae, Stephanodiscaceae, Anomoeoneidaceae each with 1 species respectively presented in the studied sites. High population densities of species were observed in the cold seasons.