The past decade has witnessed large fluctuations in the composition of phytoplankton populations in Lake Kinneret. Numerous field and laboratory studies and modeling of the data thereof were performed in an attempt to reveal the effects of abiotic and biotic parameters on the temporal and spatial phytoplankton population dynamics. However, failure to understand and predict events such as the intensification of toxic cyanobacterial blooms over the last decade, or large fluctuations in the composition of the assemblage is intriguing. There are numerous examples and a growing body of evidence that communication within and between aquatic populations plays a major role in impacting the spatial and temporal population dynamics in water bodies. In this study, we examine the allelopathic relations between the three toxic cyanobacteria: Cylindrospermopsis raciborskii, Aphanizomenon ovalisporum and Microcytosis.aeruginosa viewed blooming in Lake Kinneret in the last decade, In order to understand how these relationships affect the composition of phytoplankton populations in the water body. Results of Laboratory physiological experiments conducted in this study using qPCR analysis as well as field data sampled in the lake reveal that the Summer – spring blooming M.aeruginosa outcompetes C.raciborskii by allelopathic factor secreted to the water body, and at the same time does not show superiority over A.ovalisporum. The relationship between these three organisms may affect the composition of phytoplankton populations and the general food web.