Aquatic ecosystem consists large numbers of algal diversity. The aim of the present study is to explore the spatial and temporal variations of microalgae diversity in Lake Hawassa. 288 water samples in 45mL sterile glass bottles were collected from 14 sites during three seasons. All collected samples were preserved in 4% formalin solution and identified using inverted microscope. The result revealed that 63 microalgal species belonging to five classes, Chlorophyceae, Cyanophyceae, Bacillariophyta, Euglenophyceae and Cryptophyceae. The Chlorophyceae (46 %) members were dominant followed by Cyanophyceae (26.9 %) and Bacillariophyceae (23.81%) both spatially and temporally. Cylindrospermopsis(RA= 33.7%) and Microcystis aeruginosa(RA=21.2%), were abundant in all the sampling sites and seasons. These two species are primary toxin- producing cyanobacteria can have a negative impact on aquatic food webs and human use of freshwaters. However Chlorophyta are dominant it is indicators of good water quality. PH varied from 7.2-8.0; 8.5-9.3; and 7.1-7.8 during the winter, spring and summer seasons respectively. Annual mean transparency was 56.9-83.4 in all 3 seasons. In all three seasons high diversity index was recorded during spring season and lower diversity in winter season. There was a positive relation between water PH, transparency
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