Typically, Pyramimonas cells appear as small planktonic flagellates. Small benthic cysts are known for a few species, mostly from freshwater or tidepool habits.

The flagellate cells may be as little as 5 or as much as 50 micrometers long. The diagnostic shape is a four-lobed pyramid, although the cells are fragile and easily disrupted and therefore this shape may be lost in some preparations.

Four flagella (eight or even sixteen in a few species) emerge from a pit in the center of the pyramid base. A large chloroplast takes up most of the cell volume, and a large pyrenoid with surrounding starch grains may take up most of the chloroplast volume in the posterior part of the cell.

Cysts, when present, are formed from single cells and rarely are much larger than the cell from which it formed. A thick wall is present that may or may not be ornamented and does not contain sporopollenin. Cyst rupture releases up to four flagellate cells.

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