The species now placed in the Xanthophyceae were formerly included in the Chlorophyceae.[8] In 1899, Lüther created the group Heterokontae for green algae with unequal flagella. Pascher (1914) included the Heterokontae in the Chrysophyta. In 1930, Allorge renamed the group as Xanthophyceae.
The monadoid (unicellular flagellates) and also sometimes the amoeboid species have been included by some authors in the Protozoa or Protista,[9][10] as order Heterochloridina (e.g., Doflein and Reichenow, 1927-1929[11]), as class Xanthomonadina, with orders Heterochloridea and Rhizochloridea (e.g., Deflandre, 1956[12]), as order Heterochlorida (e.g., Hall, 1953,[13] Honigberg et al., 1964[14]), as order Heteromonadida (e.g., Leedale, 1983[15]), or as subclass Heterochloridia (e.g., Puytorac et al., 1987[16]). These groups are called ambiregnal protists, as names for these have been published under either or both of the ICZN and the ICN.
AlgaeBase (2020)
Xanthophyceae have been divided into the following five orders in some classification systems:[17]
Order Vaucheriales (e.g., Vaucheria) - siphonous organization; sexual reproduction oogamous
These are the same orders of the classification of Ettl (1978),[25] an updated version of the classic work by Pascher (1939). Ultrastructural and molecular studies shows that the Mischococcales might be paraphyletic, and the Tribonematales and Botrydiales polyphyletic,[26] and suggests two orders at most be used until the relationships within the division are sorted.[27]
Maistro et al. (2009)
Informal groups, according to Maistro et al. (2009):[28]
Botrydiopsalean clade
Chlorellidialean clade
Tribonematalean clade
Vaucherialean clade
Unicellular flagellates, amoeboid and palmelloid taxa were not included in this study.