AbstractIn this study, we aim to investigate how the functional properties of microalgae help to delineate the major groups of aquatic habitats. Using functional trait-based and Reynolds’ functional group-based approaches similarities of the microalgal flora of all aquatic habitats occurring in Hungary were compared. The habitats covered the whole size spectrum of standing waters (10^-2–10⁸ m²) and water currents (watershed: 10²–10¹¹ m²), , limnological and chemical properties. Both functional trait-based and functional group-based habitat classifications overrode the hydromorphology-based typology, however, functional group-based clusters showed closer resemblance to limnological-hydromorphological types than clusters created by trait-based approaches both for qualitative and quantitative data. Most of the aquatic habitats that have similar limnological characteristics showed resemblance in the functional properties of their microflora. Rivers and river-related habitats were the most diverse functionally. These were followed by standing waters with extended macrophyte coverage. The small, unique habitats displayed the lowest functional richness. The occurrence of several functional groups in some extreme habitats implies two alternative explanations: first, the habitat template of the groups is wider than defined in the original description; second, detailed information on the autecology of species assigned to a functional group necessitates the creation of new groups specific for the unique habitats.