Two new species of centrohelid heliozoans Acanthocystis costata and Choanocystis symna from a freshwater lake on Valamo Island and a freshwater pool in St. Petersburg (North-Western Russia) were studied with light and electron microscopy. Sequences of 18S rDNA were obtained for both species. Choanocystis symna has dumbbell-shaped plate scales (4.4–5.0 × 1.62–1.90 μm) and spine scales (3.9–6.7 μm) bearing from 3 to 5 (usually four) short teeth on the distal end. Acanthocystis costata has oval plate scales (1.3–3.7 × 0.9–1.9 μm), bearing numerous granules as well as radial slits and spine scales (2.1–9.5 μm) with 4–6 teeth on the distal end. Acanthocystis costata and Acanthocystis nichollsi are similar in having slit-bearing plate scales and group together on the 18S rDNA tree. The presence of large particles of unknown nature was observed in food vacuoles of Acanthocystis costata.