Small algae are the trophic basis in both marine and freshwater ecosystems. The identification of tiny microorganisms and place of their origin is laborious but necessary. This paper consists of a literature review of 17 species of planktonic algae, with a discussion of taxonomic problems. We also clarify whether these 17 species are non-native, invasive or cryptogenic species, with an indication whether they had been recognised as ‘alien’ in Europe. According to our observations, areas colonized by small and alien algal species, were anthropogenically altered. There were: systems with heated waters (‘heated islands’), which imitated tropical conditions; highly eutrophic to hypereutrophic water ecosystems, easily colonized by alien species, fishponds with intense fish cultivation, where alien species of fish are/had been introduced, which carried also other alien organisms; and inland water ecosystems with high salinity or high conductivity e.g. pits inundated by mine waters, imitating sea or brackish conditions acting as hubs of migration of alien species adapted to brackish or saline waters. We have prepared a map showing areas inhabited by alien species, both of documented places and hypothetical ones, where we would expect alien species to occur.