Taxonomic problems: Formerly, genera and species of cryptomonads were identified on the basis of characters such as number of ejectosome rows and plastid color. These features are useless, and are being replaced with a set of characters based primarily on periplast and pyrenoid ultrastructure. Very few algae that bear the name Cryptomonas have been examined with respect to these characters. Hence, a name applied to an illustration or culture may be misapplied at the species or even the genus level.

Some species frequently used in experimental work have never been formally identified. For example, "Cryptomonas phi" and "Cryptomonas theta" are more correctly written "Cryptomonas strain [Greek letter phi]" and "Cryptomonas strain [Greek letter theta]"; the Greek-letter strain designations were those applied to the strains by the original collector.

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