We studied the temporal phytoplankton community pattern ofthe deep crater Lake Hayq in the highlands of Ethiopia from October 2007 to October 2008. Earlier sporadic surveys indicated that the phytoplankton community was predominantly characterized by heavy diatoms, which characteristically suffer from rapid sedimentation. The trophic status of Lake Hayq was reported to have changed from oligotrophic to eutrophic in 1992. The present study addresses the potential reasons for the diatom dominance as well as causes of the trophic change. Net and integrated water samples were used for determination of physico-chemical parameters and phytoplankton biovolumes. Our results revealed that diatoms and chlorophytes dominated during most of the study period in Lake Hayq and seem to be favored by the mixing regime of the water body, which can be described as partial atelomixis with daily mixing of the epilimnion maintaining the algae within the euphotic depth via regular re-suspension. However,the epilimnion may be decoupled from the hypolimnion by a seasonal chemocline. Nutrients were notlimiting in the lake with an overall mean concentration of soluble reactive phosphorus of 22 g L-1 and total phosphorus of 58 g L-1 and of dissolved inorganic nitrogen of 305 g L-1, with ammonium being the primary form. In the 1940s only diatoms were reported, but since the 1990s other phytoplankton groups and taxa have become relevant. Canonical correspondence analysis showed that chlorophytes were mainly associated with nutrients and rainfall, euglenophytes with elevated alkalinity and the diatoms with silica and zooplankton. Chlorophyll a as measure of total phytoplankton biomass was significantly influenced by seasonality and underwater light supply, reflecting the significant role of atelomixis in persistent occurrence of heavy taxa in the epilimnion. The lake is still categorized as a eutrophic system, demonstrating that the trophic change reported in 1992 was not short-lived. In addition to changes in the catchment the eutrophication process was probably primarily triggered by a previous introduction of Tilapia in the lake, causing a cascading effectin the food–web interactions. This implied thatthe phytoplankton composition and biomass of this tropical deep tropical lake can be controlled through biomanipulation, as has been demonstrated for temperate lakes.