The genus Clathromonas comprises solitary, colourless flagellates, covered by two types of scales: round to oval inner holey plate scales with large holes of varied shape relative to intervening material; and more complex three dimensional, basket-like scales built of a very open meshwork, of varied shapes, often present in addition to or instead of holey plate scales – these may be crown scales, chair-like or tower-like. Simple spine scales with entire bases (typical for the genus Paraphysomonas) are absent. The cells bear two flagella of unequal length. They are attached to the substratum via a posterior stalk. 

Clathromonas siliceous structures. A. Eliptical, perforated plate scale with a central spine one of the forms is has (C. takahashii). B. Complex, perforated, three-dimensional crown scales (C. cf. butcheri). C. Morphologically complex pyramidal scale (C. eiffelii).