In a shallow hypertrophic lake, species richness of phytoplankton was very high (174-223 taxa, yearly) but values of Shannon-Weaver index were very low (0.04-1.38). Perennial blooms (2.1×10⁷-11.6×10⁷ ind.·L^-1) of microcystin-producing (up to 123.6 μg intracellular MCs·L^-1 in 2006, and 43.8-57.3 μg·L^-1 in 2008-09) cyanobacterium Planktothrix agardhii and the time of their appearance affected phytoplankton species richness (34-66% loss) and diversity (4-9 fold decrease in the values of Shannon-Weaver index). Short-term mass development of anatoxin-a-producing cyanobacteria (Dolichospermum spp. and/or Cuspidothrix issatschenkoi) did not influence algal biodiversity.