Cylindrospermopsis raciborskii and its highly similar relatives Raphidiopsis species have been recognized as globally invasive and expansive filamentous cyanobacteria causing water blooms. Reports on C. raciborskii/Raphidiopsis species and their harmful metabolites such as hepatotoxic cylindrospermopsins (CYNs) in Chinese waters have been increasing, but mostly restricted to the southern regions of China. To further explore the existence and distribution of C. raciborskii in China, six water samples from Beijing city were morphologically and molecularly examined. Five samples of the six were shown to have Cylindrospermopsis filaments with straight and spiral morphotypes. PCR detection targeting on Cylindrospermopsis/Raphidiopsis specific 16S rRNA gene region also showed the positive amplification, and such amplifications were confirmed by sequencing and phylogenetic analysis. As well, three of the five Cylindrospermopsis containing samples were shown to have cyrJ-a gene of CYN synthesis gene cluster. The results represented the presence of toxic Cylindrospermopsis at the most northern line in China so far, indicating rapid expansion of this harmful invasive cyanobacterium. It is strongly suggested that the monitoring on C. raciborskii/Raphidiopsis species and their production of cylindrospermopsin should be emphasized in Beijing and even more northern parts of China.