Abstract: Chroococcidiopsis, a unicellular cyanobacterial genus, distributes worldwide, and was found in extreme environments, but no Chroococcidiopsis species were reported from China. In this study, we successfully isolated a Chroococcidiopsis strain, encoded CHAB1690 from the Taihu Lake. This strain was morphologically similar to the hot spring species Chroococcidiopsis thermalis, however, low similarity of the 16S rRNA gene sequences (91%) and habitat difference distinguish this strain from C. thermalis. Including the Chroococcidiopsis CHAB1690 strain in the present study, the phylogeny based on the 16S rRNA gene sequences revealed that Chroococcidiopsis is a polypheletic genus, and the reported Chroococcidiopsis species need thoroughly polyphasic reexamination.