Cyanobacterial taxonomic studies performed by using the modern approaches always lead to creation of many new genera and species. During the field survey for cyanobacterial resources in China, a filamentous cyanobacterial strain was successfully isolated from a microbial mat attached to rock surfaces of the Ganfu Channel, Jiangxi Province, China. This strain was morphologically similar to the cyanobacterial taxa belonging to the genera Microcoleus and Phormidium. The phylogenetic analyses based on 16S rRNA gene sequences showed that this strain formed a well-supported clade, close to the filamentous genera Microcoleus, Tychonema, and Kamptonema. The maximum similarity of 16S rRNA gene sequence of this strain with the related genera was 95.04%, less than the threshold for distinguishing bacterial genus. The ITS secondary structures also distinguish this strain from the related cyanobacterial genera. Therefore, combined with morphology, 16S rRNA gene sequence, and ITS secondary structures, a novel cyanobacterial genus here as Microcoleusiopsis was established, with the species type as Microcoleusiopsis ganfuensis.