Motile cells of Pyramimonas species are covered with up to four layers of submicroscopic scales made of polysaccharides. Details of scale structure help separate Pyramimonas species from each other and from species of Halosphaera.

The flagellate cell cytoskeleton is based on a subtly asymmetrical array of four flagellar bases and four microtubular roots. The degree of cytoskeletal asymmetry is one of the features that separates the subgenera. The overall arrangement, especially in the subgenus Trichocystis, closely resembles Halosphaera. However, the "spline-MLS" root system present in Halosphaera is missing from all Pyramimonas species. A Halosphaera-like duct system is present, but the lumen of the duct is usually filled with scales (hence the term "scale reservoir"), and there is no evidence that the duct is used to capture food.

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