Cryptomonas cells appear as free-swimming small monads, from 5 to 30 micrometres long. In a few species, the cells may settle and form gelatinous colonies.

The cells are roughly bean-shaped. They appear naked, but actually have a thin cell covering ("periplast") divided into plates. Despite the periplast, cells are fragile.

Two flagella project anteriorly from a lateral insertion point. Below the insertion are two to several rows of shiny dots. These are ejectile organelles ("ejectosomes") of uncertain function. Their presence in this position is absolutely diagnostic for cryptomonads. One or two plastids take up most of the cell volume. These plastids contain significant amounts of chlorophylls (green), carotenoids (yellow to orange), phycocyanin (blue) and phycoerythrin (red), and hence can be any color. Two protruding pyrenoids may be seen, one on each plastid. Other cryptomonad genera have different pyrenoid arrangements.

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