The invasive cyanobacterial species Cylindrospermopsis raciborskii is able to produce cylindrospermopsin (CYN) that cause serious damage to human health. The published studies have showed that C. raciborskii has been widely distributed in China, and appeared to be a common species in southern China. However, its origin and toxicity potential are still unknown. In this study, ten strains of C. raciborskii isolated from Qiandenghu Lake (QDH), Guangdong Province were used to observe their growth, morphology, toxin production and phylogeography based on nifH and rpoC1 genes. Our results showed that filaments of all C. raciborskii strains were straight. Apical heterocysts were observed in all C. raciborskii strains except the strain QDH1 and akinetes were also commonly appeared. The average filament length and width of ten strains ranged from 41.0 to 77.7 μm and from 2.433 to 3.125 μm, respectively, with a significant difference between strains. The specific growth rates of the 10 strains were also significantly different, ranging from 0.075 to 0.174 d^-1. PCR analysis showed that only QDH7 gave positive amplification with six CYN synthesis genes. The strain was further analyzed by LC-MS/MS and confirmed to mainly produce deoxy-CYN isomer with the concentration of 1745.19 ng/mL. Phylogenetic analysis suggested that C. raciborskii from Qiandenghu Lake has high homology with the Australian, European and other Chinese strains, but the toxin-producing strains and non-toxin-producing strains in Qiandenghu Lake cannot be distinguished by rpoC1 and nifH genes. This study demonstrated the existence of CYN-producing C. raciborskii in water bodies of Guangdong Province, which highlights that it is necessary to prevent the ecological risks related to the newly emerging toxic cyanobacterial bloom.