Most members are unicellular flagellates, with either two visible flagella, as in Ochromonas, or sometimes one, as in Chromulina. The Chromulinales as first defined by Pascher in 1910 included only the latter type, with the former treated as the order Ochromonadales. However, structural studies have revealed that short second flagellum or at least a second basal body is always present, so this is no longer considered a valid distinction. Most of these have no cell covering. Some have loricae or shells, such as Dinobryon, which is sessile and grows in branched colonies. Most forms with silicaceous scales are now considered a separate group, the synurids, but a few belong among the Chromulinales proper, such as Paraphysomonas.
Some members are generally amoeboid, with long branching cell extensions, though they pass through flagellate stages as well. Chrysamoeba and Rhizochrysis are typical of these. There is also one species, Myxochrysis paradoxa, which has a complex life cycle involving a multinucleate plasmodial stage, similar to those found in slime molds. These were originally treated as the order Chrysamoebales. The superficially similar Rhizochromulina was once included here, but is now given its own order based on differences in the structure of the flagellate stage.
Other members are non-motile. Cells may be naked and empeded in mucilage, such as Chrysosaccus, or coccoid and surrounded by a cell wall, as in Chrysosphaera. A few are filamentous or even parenchymatous in organization, such as Phaeoplaca. These were included in various older orders, most of the members of which are now included in separate groups. Hydrurus and its allies, freshwater genera which form branched gelatinous filaments, are often placed in the separate order Hydrurales but may belong here.