Abstract: Along the rapid development of molecular biology technology, the cyanobacterial taxonomy is also experiencing great development and improvement, and many novel cyanobacterial taxa from different ecosystems were described. Coleofecosciculaceae is a new family established by Komárek et al. in 2014, which was separated from the Microcolleus-like group. However, the taxonomic studies and basic knowledge of this family are not involved in China. In this study, four filamentous cyanobacteria were successfully isolated from the microbial mats samples collected in Zhejiang Province, China. These strains were morphologically similar to the species of the family Coleofasciculaceae. The molecular characteristics and phylogenetic analysis based on 16S rRNA gene and 16S—23S ITS secondary structure showed that these strains formed well-supported phylogenetic evolutionary clades with Pycnacronema and Wilmottia, respectively. We used a method combination of all evidence composed of molecular characters, morphological, and ecophysiological data for taxa delimitation of Pycnacronema and Wilmottia. The family Coleofasciculaceae was firstly recorded here in China, and Pycnacronema and Wilmottia, were also the new recorded genera in China. In this paper, the result not only describes the history of the family Coleofasciculaceae but also introduces and discusses the modern cyanobacterial taxonomic system including its on-going process, current results and development trend. These positive results can greatly advance the progress of cyanobacterial taxonomy and increase the abundance of cyanobacterial species in China.