Halosphaera species are separated from each other based on differences in the ultrastructural morphology of scales on the flagellate cell, on differences in the ornamentation of the phycoma outer wall, and on differences in the number of flagellate cells produced in a phycoma. The last of these three characters may be less reliable than the other two.

Halosphaera flagellate cells are difficult to separate from those of Pyramimonas. At the electron microscope level, Halosphaera species have a slightly different set of scale features, and have a multilayered structure associated with the broad microtubular root (the multilayered structure is absent from the examined species of Pyramimonas).

Molecular data would help separate the species of Halosphaera from each other and from Pyramimonas.

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