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Three species are currently recognised in this genus. The type species is ''Collodictyon triciliatum''. A second species - ''Collodictyon sparsevacuolatum'' - named by Skuja is also recognised. This latter species is found in freshwater in the [[United States]] and [[Europe]]. A third species ''Collodictyon sphaericum'' has been described but its description is in doubt. A fourth species - ''Collodictyon hongkongense'' - has been described by Skvortzow but this description is considered inadequate and this species is regarded as being of dubious validity. <ref>{{cite web | author=MD Guiry in Guiry MD & Guiry GM 2012 | title=Collodictyon HJ Carter, 1865: 289 | work=AlgaeBase. World-wide electronic publication | publisher=National University of Ireland | location=Galway | url=http://www.algaebase.org/search/genus/detail/?genus_id=45305 | accessdate=28 April 2012}}</ref>
Along with another protist - ''[[Diphylleia (protist)|Diphylleia]]'' - this organism appears to be only distantly to the other eukaryotes.<ref name=Zhao2012/><ref>[http://www.livescience.com/19955-ancient-protist-kingdom.html Live Science Strange, Organism Has Unique Roots in the Tree of Life], by Jennifer Welsh, 29 April 2012</ref> They share some morphological features with the species currently placed within the [[Excavata]]. However this latter clade is considered to be polyphetic and in need of resolution. For this reason even inclusion of this genus within the excavates may not assist in understanding its phylogenetic position.
Brugerolle has proposed a family, ''[[Collodictyonidae]]'' for this [[genus]] and ''Diphylleia''.<ref name="Brugerolle"/>
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