Atelomixis influences phytoplankton composition in regions where day–night temperature variations are high. Although this physical process is shown as the most important driver in a number of tropical–subtropical lake systems, information on tropical high-mountain lakes is largely lacking. We therefore studied the phytoplankton community composition and the underlying limnological variables of the atelomictic tropical high-mountain Lake Wonchi (Ethiopia) for 13 months. Nutrient levels indicated oligotrophic conditions with ammonium being the primary nitrogen form. The phytoplankton community comprised 53 taxa distributed in five taxonomic divisions, which could be assigned to 15 codas based on phytoplankton functional group classification. Partial atelomixis and low nutrient concentrations seemed to be key variables in structuring phytoplankton community composition, which was quite stable and characterized by high diversity of heavy, immobile and fast-sinking planktonic desmids of the N A codon during mixing followed by diatoms (MP codon). A near-monospecific bloom of Peridinium cinctum (Lo codon) prevailed before the onset of lake turnover in December 2011 with conditions of nutrient depletion, which was later followed by the functional groups F–J during the episode of complete mixing and then replaced by the N A codon. Non-metric multidimensional scaling resulted in a 2-dimensional solution, which revealed clear segregation of phytoplankton community to five groups. Mixing regime of the water column, conductivity, total phosphorus, ammonium and zooplankton had significant influence on the observed seasonal pattern.