The article presents the results of the investigations on diversity and quantitative structure of phytoplankton of different types of aquatic ecosystems within the Republic of Moldova during 2010-2015. The invasive species (native) Merismopedia tenuissima Lemmermann 1898, Synechocystis aquatilis Sauvageau 1892 and Aphanizomenon flos-aquae Ralfs ex Bornet & Flahault 1886 from phytoplankton composition were identified. The potential growth of these phytoplankton species can lead to algal blooms. Following our investigations, it was established that the biomass of invasive Cyanophyta planktonic species during their intense development can account for about 80-90% of the number of species and for about 40-60% of the phytoplankton biomass.