Members of the genus Mallomonas are solitary, free-living flagellates, surrounded by an envelope of silica scales. Scales consist of a perforated basal plate, often overlained by secondary patterns. In most species, scales are tripartite, comprising a dome, shield and flange.

In most species some or all scales bear silica bristles. These are formed as flat elements and then roll up into shape. Bristles either glued to the scale (primitive species), or articulated by a special foot in the concavity of the dome (when present). The bristles are smooth or serrated, and the tips may be intricately shaped (bifurcated, helmet-shaped).

Identification of Mallomonas species is generally based on the ultrastructure of silica scales and bristles, using electron microscope. Only several species could be identified without doubs by means of light miscroscope. Based on scale and bristle ultrastructure, Mallomonas taxa are traditionally classified into the sections and series.

A. Mallomonas cell covered with armour of silica scales (M. akrokomos). B. General morphology of silica scale (M. leboimei). AF = anterior flange; D = dome; PB = proximal border; PF = posterior flange; S = shield; V = V-rib. C. Serrated bristle (M. caudata). D. Helmet bristle (M. heterospina)