The cell body of centrohelid heliozoans is covered with a layer of scales. These scales have species-specific morphology and, since they present in the trophic stage of the cell cycle can be termed “trophic” scales. Several species are known to form cysts; during this process they can produce specific “cyst” scales, different from trophic scales. The present paper describes morphology of cyst scales in two species of centrohelid heliozoans: Raineriophrys erinaceoides and Raphidiophrys heterophryoidea. The latter species has two types of cyst scales: scales of the first type resemble trophic scales in general structure but, their borders are broad, flattened and not enrolled. Scales of the second type are polygonal and connected to each other by special teeth, forming a single layer organized in a jig-saw puzzle-like manner. In Raineriophrys erinaceoides only one type of cyst scale was found. These scales are polygonal and completely different from trophic scales. It is unclear whether these scales form a puzzle-like layer or just overlap each other. Newly excysted individuals keep remnants of cyst scales in their cell coverings and at this stage cyst scales can easily be noted. The morphology of the cyst scales reported here is unlike any other previously reported.