Heliozoan amoebae almost certainly represent a polyphyletic group, assembled on the basis of radially symmetrical cells with protruding axopodia and/or filopodia. Individual groups of heliozoa, however, have different mitochondria (the flattened, tubular and discoidal cristae types all are represented), different organization of the axopodial/filopodial axonemes, and different sites of axonemal attachment (and presumed nucleation). Centrohelid amoebae with a trilaminate centroplast probably represent a monophyletic group (clade), which is only distantly related to other heliozoa.

Species identification in Raphidiophrys, as well as in other genera of scale-producing centrohelid heliozoa, is entirely dependent on the detailed morphology of the scales as viewed with the electron microscope. Keys and catalogs that do not use the ultrastructural characteristics of the scales are not to be trusted.

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