Investigations carried out on Lake Dojran, fYR Macedonia, during the spring-autumn seasons in 2015 have been focused on detecting the degree of eutrophication in the lake, successive algal flora changes in the plankton communities and eventual presence of cyanotoxins (free microcystins) in the water. The obtained results revealed a co-existence of nine Microcystis species in the lake (M. aeruginosa, M. botrys, M. flos-aquae, M. ichthyoblabe, M. novacekii, M. protocystis, M. smithii, M. viridis and M. wesenbergii), with domination of the pan and neo-tropical species M. protocystis, again confirmed in a European lake. Results also corroborate the necessity to change the accepted morphospecies concept into separation of Microcystis taxa as distinct species which are clearly delimited according to their constant morphological features. Toxicity analyses demand for a specific and targeted investigation, since the toxin production and presence depends on many factors, and the toxin dynamics including the highest peaks may be easily overlooked if other issues are in the focus of the performed monitoring. Detected values for free microcystins in the water reached 2.84 µg L-1 microcystin-LR equivalents.