The eustigmatophycean algae are unique in the Heterokontophyta to show greenish color. All eustigmatophycean algae are unicellular coccoid. The Eustigmatophyceae is a small group including less than 20 species. However, many species classified into the Xanthophyceae may be really members of the Eustigmatophyceae. The eustigmatophycean algae inhabit on soil, in freshwater or marine. The only marine genus, Nannochloropsis is sometimes coled as "marine chlorella" (but Chlorella is distantly related) and widely used for fish farming.

The cell is non-motile and enclosed by cellulosic cell wall. The chloroplasts with scattered plastid nucleoid include no girdle lamella. Many species possess bulging pyrenoid covered by vesicles including lamellate material (β-1,3-glucan?). This organelles (lamellate vesicles) are also dispersed in cytosol, and can be recognised as reflactile granules under light microscopy. The Eustigmatophyceae lack chlorophyll c and fucoxanthin, thus they show greenish color. The flagellate cell possesses one or two flagella. Most flagellate cells have a large, cytosolic, anterior stigma and a unique flagellar swelling at the anterior (no. 2) flagellum. However, the eustigmatophycean algae without such characters are recently reported (Pseudostaurastrum, Pseudotetraëdriella).