The genus Pompholyxophrys includes amoebae which have a spherical body, fine radiating pseudopodia, and a layer of adhering siliceous “perles.” These organisms are normally regarded as a type of heliozoon. Ultrastructural examination of P. punicea reveals that those characters associated with well characterized heliozoa, such as microtubular axonemes and extrusomes, are lacking. The species has much in common with nucleariid filose amoebae with which it, and the related genus Pinaciophora, are regarded as having affinities. The species P. punicea is rare, and this study was made possible by the application of techniques developed for the ultrastructural examination of single cells. The assessment of protistan diversity and interrelationships relies heavily on the use of ultrastructural characters. Although techniques that are based on the examination of a small number of individual cells have limitations, they do allow rare organisms to be included in the re-evaluation of protistan systematics.