The genus name of Treubaria is in honour of Melchior Treub (1851–1910), who was a Dutch botanist.

Currently, the taxonomy of green algae is in flux because morphological characteristics do not align with phylogenetic relationships.

Phylogenetically, Treubaria forms a close relationship with Cylindrocapsa, Elakatothrix, and Trochiscia.

All four genera share ultrastructural features such as pyrenoids where the matrix is penetrated by cytoplasmic invaginations, and Cylindrocapsa produces quadriflagellate zoospores.

However, the genera share litle else in common, making a coherent classification difficult.