Four strains of non-encysting amoebae were isolated from organs of freshwater fishes and characterized using light and electron microscope. Morphology of three clonal strains was consistent with amoebae which had already been described from water habitats. Two strains, one isolated from kidney tissue of common goldfish, Carassius auratus (Linnaeus, 1758), and the second one from brain of chub, Leuciscus cephalus Linnaeus, 1758, were identified with Vannella platypodia (Gläser, 1912) Page, 1976. Both strains were identical, except for the length of glycostyles. The strain isolated from the liver of perch, Perea fluviatilis (Linnaeus, 1758), was assigned to the genus Vexillifera Schaeffer, 1926 as Vexillifera expectata sp. n. The taxonomic position of the fourth non-encysting strain could not be safely established, although it shares some trophic cell structures with protostelids (Protostelia, Eumycetozoea). We present its detailed description here also to demonstrate that amoeba stages of this type of organisms are capable to infect fishes.