Despite the high importance of shallow thaw ponds (thermokarst lakes) of Western Siberia in both surface coverage and carbon dioxide and methane emission to the atmosphere, their planktonic component remains poorly characterized. This work reports the first results of phytoplankton analysis of thaw lakes and ponds sampled during spring flood, open water season and ice formation. The lakes, located within the discontinuous/sporadic permafrost (66xN), are shallow (0.5-1.5 m depth), acidic (4.0 j pH j 6.1) and highly organic (10-40 mg.L x1 of DOC) with low concentrations of total dissolved solid (10-30 mg.L x1). In the plankton community of 20 lakes of variable size (from 700 m 2 to 1.8 km 2), we identified 134 taxa of algae with the dominance of green algae (33-60% of total), cyanobacteria (11-14%) and dinoflagellates (7-14%). The total cell number (N) ranged from 20 to 83 million cell.L x1 and the biomass (B) ranged from 0.1 to 37 mg wet .L x1 with the dominance of green algae, Dinophyta and Charophyta Ulothrix spp., Bambusina brebissonii. A Principal Component Analysis (PCA) revealed two possible factors responsible for phytoplankton variation: dissolved inorganic carbon, positively acting on cell number and the biomass of cyanobacteria, and DOC, Si and Fe, controlling the number of diatoms and green algae. In August, there was a general increase of both N and B as pH increased. Colony-forming cyanobacteria and green algae with thick capsules were highly abundant during all seasons. The specific acidic and organic-rich context of the shallow thermokarst waters subjected to full freezing in winter is one of the major factors limiting both the biodiversity and the biomass of the phytoplankton in these water objects.