The cryptomonads are a small group of flagellates, most of which have chloroplasts. They are common in freshwater, and also occur in marine and brackish habitats. Each cell is around 10-50 μm in size and flattened in shape, with an anterior groove or pocket. At the edge of the pocket there are typically two slightly unequal flagella.

Cryptomonads distinguished by the presence of characteristic extrusomes called ejectisomes, which consist of two connected spiral ribbons held under tension. If the cells are irritated either by mechanical, chemical or light stress, they discharge, propelling the cell in a zig-zag course away from the disturbance. Large ejectisomes, visible under the light microscope, are associated with the pocket; smaller ones occur elsewhere on the cell.

Cryptomonads have one or two chloroplasts, except for Chilomonas which has leucoplasts and Goniomonas which lacks plastids entirely. These contain chlorophylls a and c, together with phycobilins and other pigments, and vary in color from brown to green. Each is surrounded by four membranes, and there is a reduced cell nucleus called a nucleomorph between the middle two. This indicates that the chloroplast was derived from a eukaryotic symbiont, shown by genetic studies to have been a red alga.

A few cryptomonads, such as Cryptomonas, can form palmelloid stages, but readily escape the surrounding mucus to become free-living flagellates again. Cryptomonad flagella are inserted parallel to one another, and are covered by bipartite hairs called mastigonemes, formed within the endoplasmic reticulum and transported to the cell surface. Small scales may also be present on the flagella and cell body. The mitochondria have flate cristae, and mitosis is open; sexual reproduction has also been reported.

Originally the cryptomonads were considered close relatives of the dinoflagellates because of their similar pigmentation. Later botanists treated them as a separate division, Cryptophyta, while zoologists treated them as the flagellate order Cryptomonadida. There is considerable evidence that cryptomonad chloroplasts are closely related to those of the heterokonts and haptophytes, and the three groups are sometimes united as the Chromista. However, the case that the organisms themselves are related is not very strong, and they may have acquired chloroplasts independently.