Species identification in Pyramimonas is based almost entirely upon the ultrastructural features of scales, pyrenoids and the interphase cytoskeleton. These identifications are supported by studies based on molecular sequence comparisons. Earlier systems based on such characteristics as cell size, number and location of eyespots, and prominence of pyrenoid, are not reliable. Any culture isolate that has a species name, but has not not at some time been the subject of an ultrastructural, or combined ultrastructural/molecular, examination, may be misidentified.

Pyramimonas flagellate cells are difficult to separate from those of Halosphaera. At the electron microscope level, Pyramimonas species have a slightly different set of scale features, and lack a multilayered structure associated with the broadest microtubular root of the cytoskeleton.

The earliest literature on this genus sometimes cites the genus name Pyramidomonas. The two names are synonyms, with Pyramimonas the name to use.

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