Once classified by Page (1987) in the class Lobosea subclass Gymnamoebia, they are now considered as members of the phylum Amoebozoa, class Discosea (Cavalier-Smith et al. 2004). Initially, they were dispersed among various genera and families. Probably the first reliably described vannellid was 'Amoeba platypodia' (Glaser 1912). Schaeffer (1926) included vannellid amoebae than known in three genera, all in different families: Flabellula, where he placed 'F. mira' (now Vannella mira); Rugipes, where he placed R. vivax (now Clydonella vivax), and Unda with a not yet redescribed species U. maris.
Wohlfarth-Bottermann (1960) added a fourth genus to this collection: 'Hyalodiscus simplex' (now Vannella simplex). Bovee (1965) established the genus Vannella, for three of these species -'Flabellula mira', 'Amoeba platypodia', and 'Hyalodiscus simplex'; he redefined the genus Flabellula, restricting it to amoebae producing trailing uroidal filaments and short conical pseudopodia, neither character being present in Vannella. However, he considered the genus Vannella as closely related to flabellulid amoebae, so placed it in the family Flabellulidae; later he created a separate subfamily Vannellinae within Flabellulidae (Bovee, 1970).
F. C. Page initially did not accept the genus Vannella and provided a new diagnosis for Schaeffer's species 'Flabellula mira' (Page, 1968). The same paper described a new species, Rugipes placidus, thus accepting the validity of Schaeffer's genus Rugipes. However, a year later Page accepted Bovee's revision of Flabellula and noted that species redescribed by him as Flabellula must be identified as Vannella; he also established the genus Platyamoeba to accommodate Rugipes placidus and a newly described species, P. stenopodia (Page, 1969). He belived these amoebae to be the closest relatives of thecamoebids, not flabellulids, so placed Platyamoeba in the family Thecamoebidae. Pussard (1973) created a genus Pessonella for a single species of Vannella-like amoeba - Pessonella marginata, possessing characteristic lobes on the surface of the frontal hyaloplasm, placing it in the family Mayorellidae; later Page (1976) transferred all these genera into Thecamoebidae. Sawyer (1975) established two more genera of vannellid amoebae - Clydonella and Lingulamoeba - to accommodate Vanellla-like amoebae differing from both Vannella and Platyamoeba in locomotive morphology and floating form. The type species of Clydonella was Schaeffer's Rugipes vivax. Differentiation of these two genera from Vannella and Platyamoeba was difficult, since no ultrasructure was provided at the time of description. Page (1983) considered Lingulamoeba a junior synonym of Platyamoeba (the combined name Platyamoeba leei was provided), and listed Sawyer's Clydonella among 'other genera of Thecamoebidae'. Later Page (1987) started to consider all these genera (and Pessonella) as possible synonyms of Vannella or Platyamoeba Page (1988). His revised classification of naked amoebae raised the rank of Bovee's subfamily Vannellinae to family Vannellidae, which included only two genera: Vannella and Platyamoeba (Page, 1987). Later Rogerson and Patterson (2002) included Clydonella and Pessonella in the family Vannellidae together with the little-known genera Discamoeba Jahn, Bovee and Griffith 1979 and Unda Schaeffer 1926, but omitted the genus Lingulamoeba, thus accepting Page's suggestion that it is a synonym of Platyamoeba (Page, 1983).
These taxonomic perturbations well illustrate the difficulty of morphological systematics of vannellid amoebae. The primary reason for this is that all vannellids are flattened, fan-shaped organisms with a very limited number of light-microscopic (LM) morphological characters. Page (1983) noted that a vannellid amoeba with slender, tapering pseudopodia on the floating form can be safely classified as Vannella; however, further studies show that some vannellas do not form such pseudopodia when afloat (Smirnov 2001), while some platyamoebian floating forms may be very similar to those of vannellas (Smirnov 1999). Therefore, when electron-microscopic (EM) studies revealed clear differences in cell surface structure between the then known species of Vannella (having glycostyles) and Platyamoeba (lacking glycostyles) (Page and Blakey 1979), this cell surface structure immediately become the key, and virtually only, character used to distinguish these genera and to classify all newly discovered vannellids into one of them. Page (1979) provided a new diagnosis of the genus Vannella that included cell surface structures. However, this character was not always congruent with LM features of a species. For example, Page (1980, p.939) wrote that it was a 'considerable surprise' to find that Platyamoeba-like strain of a vannellid amoeba nowadays known as Vannella anglica possesses glycostyles.
Molecular phylogenies showed vannellid amoebae as a distinct monophyletic lineage of Amoebozoa, well separated from the other groups (Bolivar et al. 2001; Fahrni et al. 2003; Sims et al. 1999). Comprehensive analyses of amoebozoan SSU rRNA trees by Cavalier-Smith et al. (2004), Kudryavtsev et al. (2005), and Smirnov et al. (2005) strongly confirmed that all vannellids form a distinct clade on the SSU tree, consisting of four genera: Vannella, Platyamoeba, Clydonella, and Lingulamoeba. Peglar et al. (2003) provided SSU rRNA sequences and ultrastructure of Clydonella and Lingulamoeba, which confirmed the validity of both genera and the monophyly and distinctiveness of vannellid amoebae as a whole. However, relationship between the genera Vannella and Platyamoeba remain ill-resolved. It was shown that Platyamoeba stenopodia is not a vannellid, and is closely related with thecamoebids (Fahrni et al. 2003). Sims et al. (2002) using partial SSU rDNA sequences found that Vannella and Platyamoeba are mixed in the tree and suggested that their phylogeny is related more to LM features and to habitat (freshwater or marine) than to cell surface structure. Finally Dykova et al. (2005) obtained sequences of fish-associated vannellids identified only to genus, confirming that strains with a surface structure formerly attributed to Vannella and Platyamoeba do not form distinct clades in the tree.