[1][2] It is characterized by its red colour, the square-shaped plates of its inner periplast, its short furrow ending in a gullet, and a distinctly shaped chloroplast closely associated with its nucleomorph.

[3] Historically, Rhodomonas was characterized by its red chloroplast alone,[4] but this no longer occurs as its taxonomy has become increasingly based on molecular and cellular data.

[4][9] The first indication of Rhodomonas’ existence was Karsten's observation of its proliferation in a sample containing diatoms, seashells, stones, and the brown algae Sphacelaria.

Karsten observed that Rhodomonas contained a red chloroplast, two posteriorly-oriented flagella originating from an anterior gullet, and a large nucleus in the middle of the cell.

[4] At the time of discovery, red flagellates were previously unknown and colour was used as the identifying feature of Rhodomonas.

[4] Zimmermann later identified Karsten's “nucleus” as the cell's pyrenoid, based on its characteristic position within the cytoplasm.

[6][10] A countering argument is that Rhodomonas has historical priority as it was established before Pyrenomonas, and should continue to be used when referring to this genus.

[4][7] This is demonstrated in recent molecular phylogenies of cryptomonads, where it is established that Rhodomonas and Pyrenomonas are synonymous.

[11][12][13][14] Given how closely related these genera are, there is some uncertainty as to how distinct the genus Rhodomonas is from Rhinomonas and Storeatula.

The external component of the periplast is made up of a coarse, intertwining fibril network that is characteristic of Rhodomonas.

[4] The internal periplast component consists of small square-shaped plates arranged in longitudinal rows.

To accommodate the ejectisomes of the gullet in Rhodomonas, the anterior edges of the internal periplast plates are slightly raised.