A qualitative and quantitative study on epiphytic microalgae was carried out seasonally from November 2015 to August 2016 to follow up their community structures on aquatic macrophytes related to some physico-chemical properties of two polluted and unpolluted water bodies at Assiut, Egypt. A total of 169 species related to 64 genera of epiphytic microalgae were recorded. The most dominant algal group was Bacillariophyceae (43.2%), followed by Chlorophyceae (34.91%), Cyanophyceae (20.71%) and Euglenophyceae (1.18%). The total number of epiphytic algae fluctuated between 11.1 × 104 ind.g-1 plant dry wt. on Phragmites australis in summer at Nazlet Abdellah (polluted site) and 10.02 × 107 ind.g-1 plant dry wt. on Myriophyllum spicatum in winter at El-Wasta (unpolluted site). Some epiphytic microalgae were dominant as Pseudanabaena limnetica, Calothrix braunii, Scenedesmus acutus, and Ulnaria ulna. Others were specific on certain macrophytes as Aphanocapsa thermalis and Ulothrix sp., which grow on Phragmites australis, while Synechocystis minuscula attached itself on Myriophyllum spicatum. Analysis of PERMANOVA showed that the most important factors that induced the variation in epiphytic microalgae were the temporal variation and host plant. Water temperature, pH, nitrate, chloride, phosphate and total dissolved salts were the highest abiotic factors correlated with the variation in composition of epiphytic microalgae.
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