Introduction: Cryptomonas is a genus of small phytoflagellates. Species are common in marine and freshwater plankton, but the cells often are not found in plankton samples because the usual fixatives do not preserve them - hence the common name cryptomonads ("hidden flagellates"). The genus and its relatives have become notorious, because the cryptomonad plastid is the vestige of a eukaryotic endosymbiont, and because the confusing assemblage of structural features that cryptomonads possess has made it difficult to establish the phylogenetic relationships of the group.

Postulated global eukaryote phylogeny based on presence or (ancestral) absence of mitochondria, and shape of mitochondrial cristae. Cryptomonas belongs to the flattened clade.

Postulated phylogenetic position of Cryptomonas, inferred from molecular and morphological data. Branch lengths are arbitrary and do not reflect phylogenetic distance.

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