Polyphasic taxonomic studies have been extensively carried out in cyanobacteria, resulting in the description of numerous cyanobacterial genera and species. The present study described a new cyanobacterial genus Compactonostoc gen. nov. based on a combination of morphological, genetic, and ecological evidence. The new genus was collected from a wet rocky wall in Shennongjia Forestry District, China. Colonies of the Compactonostoc strain were usually uniseriate or only in short segments biseriate when young, and filaments became densely entangled to form a macroscopic colony when mature; however, the filaments did not form spherical colonies. The phylogenetic tree based on 16S rRNA gene sequences showed that Compactonostoc formed a unique cluster, separating from the Nostoc sensu stricto' clade and from the clades of the morphologically similar genera Komarekiella, Desmonostoc and Mojavia. The 16S-23S rRNA internal transcribed spacer (ITS) secondary structure of the Compactonostoc strain showed a unique pattern of D1-D1, Box-B and V3 helix, which distinguished it from other heterocystous genera. Compactonostoc shennongjiaensis sp. nov. was designated as the type species of the genus.