Sixteen taxa of the genera Raphidocystis, Raphidiophrys, and Pompholyxophrys from freshwater habitats in Canada, Chile, and New Zealand were studied by light and electron microscopy. Six taxa are described as new: Raphidocystis glabra, Raphidiophrys minuta, Raphidiophrys orbicularis ssp. orbicularis, R. orbicularis ssp. ovalis, Pompholyxophrys stellata, and P. ossea. New information on scale structure and arrangement based on scanning and transmission electron microscopy amplifies the taxonomic descriptions of Raphidiophrys ambigua, R. pallida, R. elegans, R. intermedia, R. marginata, R. symmetrica, Pompholyxophrys punicea, P. exigua, and P. ovuligera, which were previously imperfectly known by light microscopy only.