Centrohelid heliozoans are unciliated axopodial protists of uncertain affinities. Cell coverings (organic spicules, siliceous plate-scales and spine-scales) are the main character for their taxonomy. Phylogenetic reconstructions for this group are mostly based on the sequences of 18S rDNA. In this paper molecular and microscopical data are provided for Raphidiophrys heterophryoidea, R. drakena sp. nov., Spiculophrys agregata gen. et sp. nov. and four strains here referred to as Heterophrys-like organisms (HLOs). The family Raphidiophryidae is shown to be polyphyletic. Position of Spiculophrys is uncertain, but presumably it represents the most basal branch in the order Pterocystida. HLOs branch deeply inside the genera Acanthocystis (3 strains) or Polyplacocystis (1 strain), even though they considerably differ in morphology of the coverings from other members of these genera. The possible reasons of this phenomenon are discussed. On the basis of newly obtained sequences and EDX-analysis an interpretation of