The effect of saxitoxins (STX) on phytoplankton species is poorly understood. To date, no correlation between STX concentrations and phytoplankton physiology has been reported. We investigated the effect of STX (STX+, 0.5-10 μg L −1 total STX) and non-STX (STX−, 0.5-10 μg L −1 total STX biomass equivalent) extracts of Cylindrospermopsis raciborskii on Microcystis wesenbergii BCCUSP11, Microcystis aeruginosa BCCUSP232 (microcystin producing), Scenedesmus acuminatus UFSCar036, and Monoraphidium convolutum CMEA/UFF0201 under controlled laboratory conditions. Both STX+ and STX− extracts inhibited the cell density and specific growth rate of M. wesenbergii, M. aeruginosa, and S. acuminatus. However, the effect of STX+ extract on the phytoplankton strains was significantly higher than that of STX− extract. M. convolutum, on the other hand, was tolerant as both STX+ and STX− extracts did not significantly reduce its cell density and specific growth rate (day −1). The exposure of M. aeruginosa to STX+ and STX− resulted in higher total (intracellular and extracellular) microcystin concentration than the control. STX concentrations had a significant negative correlation with cell density and growth response of the phytoplankton strains investigated in this study. Conclusions can be made that although both STX+ and STX− extracts of C. raciborskii inhibited the growth of some phytoplankton species, the STX+ extracts were more toxic. Keywords Growth inhibition. Cyanotoxins. Phytoplankton. dc-Saxitoxin. Neo-saxitoxin. Microcystins on sodium channels in both prokaryotes and eukaryotes (Neilan et al. 2013). STX are of high ecotoxicological risk due to the toxicity they induce in fish, mussels, copepods, mammals, and birds (Landsberg 2002). A number of cyanobacteria such as Aphanizomenon flos-aquae, Cylindrospermopsis raciborskii, Lyngbya spp., and Anabaena spp. synthesize STX in freshwater ecosystems. However, the production of this group of toxins tends to be strain specific (Molica et al. 2002; Bernard et al. 2003; Wiegand and Pflugmacher 2005; Al-Tebrineh et al. 2010). The discovery that C. raciborskii produces STX and cylindrospermopsin has made it an important cyanobacterium to be monitored in aquatic ecosystems. This is due to the increased frequency of its occurrence, scientific interest, improved water quality monitoring, availability of suitable habitat, and in some cases, its invasion of new habitats (Figueredo et al. 2007; Kling 2009; Sukenik et al. 2012). The cosmopolitan and increasing distribution of C. raciborskii is easily traced to its ecophysiological adaptation and tolerance to changing physicochemical