Eustigmatophytes contain one or more yellow-green chloroplasts, which contain chlorophyll a and the accessory pigments violaxanthin and β-carotene.

Eustigmatophyte zoids (gametes) possess a single or pair of flagella, originating from the apex of the cell.

Most eustigmatophyte genera live in freshwater or in soil, although Nannochloropsis contains marine species of picophytoplankton (2–4 μm).

The class was erected to include some algae previously classified in the Xanthophyceae.

[3] Phylogeny of Eustigmatophyceae based on the work of Amaral et al 2020[5] Goniochloris Trachydiscus Vacuoliviride Pseudostaurastrum Tetraedriella Paraeustigmatos Pseudellipsoidion Characiopsiella Munda Neomonodus Pseudotetraedriella Monodopsis Microchloropsis Nannochloropsis Pseudocharaciopsis Chlorobotrys Eustigmatos Eustigmatos