Three new extinct taxa of the genus Stephanodiscus Ehrenberg (S. williamsii sp. nov., S. princeps sp. nov., S. yukonensis var. antiquus var. nov.) and four new extinct species and two new extinct varieties of the genus Cyclotella (Kutzing) Brebisson (C. iris var. insueta var. nov., C. tempereiformica sp. nov., C. distincta sp. nov., C. comtaeformica sp. nov., C. comtaeformica var. spinata var. nov. and C. praeminuta sp. nov.) are described from Upper Cenozoic lacustrine sediments of Lake Baikal (boreholes BDP-96-1 and BDP-96-2). The narrow biostratigraphic ranges of the new taxa warrant their use as index-fossil species for defining a diatom zonation, for accurate correlation and age control of Lake Baikal sediments. The comparative morphological analysis of the newly described Cyclotella taxa allowed us to trace the evolution of morphological features in these diatoms through time. The short time intervals during which the Stephanodiscus taxa existed in ancient Baikal imply that these species were unable to adapt to rapidly changing paleoecological and paleolimnological conditions caused by abrupt Pleistocene climatic fluctuations.