The changes of general number of phytoplankton in photic layer of South Baikal at permanent station near Bol'shie Koty settlement in 1988 and 2009 years differing in temperature are presented. In these years the quantitative development of phytoplankton differs greatly. In warmer 2009 general number of phytoplankton was higher, and its vertical dynamics was characterized by longer time of summer stratification. The close connection between changes of phytoplankton number and water temperature during summer is established.