The paper critically summarizes data collected on the diversity of euglenoids in fresh waters of Indonesia for more than 160 years of study. An analysis of the literature and original data showed that the flora of Euglenophyceae in Indonesia has not been studied adequately. To date, 122 species (153 intraspecific taxa) from 12 genera have been recorded in Indonesian waters. Four genera: Trachelomonas, Phacus, Lepocinclis, and Strombomonas combine 84% of the species diversity. The remaining eight genera were poorly represented in terms of species number; osmotrophic and heterotrophic euglenoids from the Indonesian water bodies are practically unknown. Most species studied are from the reservoirs of the islands of Java and Bali. The level of endemism of the Indonesian flora of euglenoids is only 4%; it is quite low compared to other taxonomic groups of algae in the region. The checklist was compiled according to the latest changes in taxonomy of euglenoids; the main synonyms are given. Here we also propose four new nomenclature combinations: Monomorphina aenigmatica f. filicauda (W. Conrad) D. Kapustin comb. nov., Strombomonas fluviatilis var. rugosa (Prescott) D. Kapustin comb. nov., Lepocinclis kriegeri (W. Conrad) D. Kapustin comb. et stat. Nov., and Lepocinclis helicoideus (C. Bernard) D. Kapustin comb. nov. The last combination was previously presented invalid and is now validated in this work .
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