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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 mitochondriaIn cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. Mitochondria are sometimes described as " cellular power plants" because their primary purpose is to manufacture adenosine triphosphate (ATP), which is used as a sourc have flate cristaCristae are the infoldings of the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes, and function in cellular respiration. They provide more surface area for cellular respiration to happe, and mitosisIn biology, mitosis is the process of chromosome segregation and nuclear division that follows replication of the genetic material in eukaryotic cells. This process assures that each daughter nucleus receives a complete copy of the organism's genome. is open; sexual reproduction has also been reported.

Originally the cryptomonads were considered close relatives of the dinoflagellateDinophyceae Noctiluciphyceae Syndiniophyceae The dinoflagellates are a large group of flagellate protists. Most are marine plankton, but they are common in fresh water habitats as well. About half of all dinoflagellates are photosynthetic, and these makes 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 heterokontColored groups Chrysophyceae (golden algae) Synurophyceae Actinochrysophyceae (axodines) Pelagophyceae Phaeothamniophyceae Bacillariophyceae (diatoms) Raphidophyceae Eustigmatophyceae Xanthophyceae (yellow-green algae) Phaeophyceae (brown algae) Colorlesss and haptophyteThe haptophytes classed either as the Prymnesiophyta or Haptophyta, are a group of algae. The chloroplasts are pigmented similarly to those of the heterokonts, such as golden algae, but the structure of the rest of the cell is different, so it may be thats, 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.