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The ecology of phytoflagellates in Finnish brown-water lakes is discussed using results from three studies. The data allow analysis of both phytoflagellate community relationships and the autecology of dominant species.Humic matter imparts a brown colour to most Finnish lakes. The consequent rapid warming of the water, shallow epilimnion and nutritional differences between epilimnion and hypolimnion are related to the migrations and nutritional pathways of flagellates in such systems. In large lakes migrations are not of such fundamental significance as in small forest lakes, where both illumination and the nutritional relationships may induce phytoflagellate migrations. The occurence of flagellates is more frequent and their dominance in the phytoplanktonic biomass is strongest in the most brown lakes, where independent motility is a particular advantage for the survival and competition of flagellates against other species.