Modern molecular biological technology has provided much information and evidence for cyanobacterial diversity. Unicellular cyanobacterial genus Geminocystis was established in 2009 by separating from Synechocystis. In this study, a cyanobacterial strain was isolated in May 2017 from Lake Yueya-a small and enclosed lake close to the Lake Qinghai. This strain shows the close similarities of 16S rRNA gene sequences to the strains of Geminocystis as over 97%,and group with the strains into a cluster in the phylogenetic tree. The keritomized content and irregular arrangement of thylakoid in cells of this strain represent the unique features of the Geminocystis genus. The Geminocystis genus is firstly reported in China, and its taxonomic and ecological notes are discussion in this study.