The presence of prokaryotic ecto- and endocytobionts in flagellated protists was investigated by literature and our own data. Cytobionts have been found in Cercomonadida, Chlorophyta, Choanoflagellida, Chrysophyceae, Cryptophyceae, Dinophyceae, Euglenophyceae, Glaucocystophyceae, Heterolobosea, Kinetoplastida, Oxymonadida, Parabasalia, Pelobiontida, Raphidophyceae, Spongomonadida,Thaumatomonadida, and Xanthophyceae. Eciobiotic bacteria occuron the cell surface of 31 species of flagellates, and endobiotic prokaryotes are found in 69 species of flagellates. The majority of endobionts are found in the cell cytoplasm (in 51 species), some of them live in thenucleoplasm (8 species), other occur in the perinuclear space (9 species). In one case endobionts were described in chloroplasts and mitochondria (Wilcox, 1985), but it was not confirmed by other investigations. Possible reasons of different frequency of cytobiont occurrence in cell compartments of a moebae, flagellates and ciliates are also discussed.