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Symbiosis of green algae with protozoa and invertebrates has been studied for more than 100 years. Endosymbiotic green algae are widely distributed in ciliates (e.g.Paramecium,Stentor, Climacostomum, Coleps, Euplotes), heliozoa (e.g.Acanthocystis) and invertebrates (e.g.Hydra,Spongilla), and have traditionally been identified as named or unnamed species ofChlorellaBeij. orZoochlorellaK. Brandt or referred to asChlorella-like algae or zoochlorellae. We studied 17 strains of endosymbionts isolated from various hosts and geographical localities using an integrative approach (nuclear encoded small subunit and internal transcribed spacer regions of rRNA gene sequences including their secondary structures, morphology, physiology and virus sensitivity). Phylogenetic analyses have revealed them to be polyphyletic. The strains examined belong to five independent clades within the Trebouxiophyceae (Choricystis-,Elliptochloris-,Auxenochlorella- andChlorella-clades) and Chlorophyceae (Scenedesmus-clade). The most studied host organism,Paramecium bursaria, harbours endosymbionts representing at least five different species. On the basis of our results, we propose a taxonomic revision of endosymbiotic ‘Chlorella’-like green algae.Zoochlorella conductrixK. Brandt is transferred toMicractiniumFresen. andZoochlorella parasiticaK. Brandt toChoricystis(Skuja) Fott. It was shown thatChoricystis minor(Skuja) Fott, the generitype, is a later heterotypic synonym ofChoricystis parasitica(K. Brandt) comb. nov. A new species,Chlorella heliozoae, is proposed to accommodate the endosymbiont ofAcanthocystis turfacea.