Effects of autumnal stratification on phytoplankton communities at different depths were studied in Lake Solumsjö, NE Sweden. Species number, Shannon-Weaver’s, Margalef’s and Menhinick’s indices as well as cluster analyses using presence-absence with abundance matrices were applied. All diversity indices used clearly indicated higher diversity in epilimnion compared to that in hypolimnion. This pattern can be explained by sole dominance of Trachelomonas volvocinopsis under predominantly anoxic conditions and high concentrations of iron and manganese below the thermal gradient. Stratification disappeared between September 29 and October 4, thus leading to homogenisation of water column and similar phytoplankton communities at all depths. Cluster analyses using presence-absence with abundance matrices turned out to be a powerful tool when studying temporal changes in phytoplankton communities as a result of stratification patterns. Two distinct clusters at depths of 0, 2 and 10 m were clearly separated: one containing algal communities during stratification and one containing algal communities after the thermal gradient disappeared. At the depth of 5 m more homogeny between phytoplankton communities under stratified and mixed conditions was observed.