The traditional cyanobacterial form-genus Aphanothece was established according to morphological criteria in the middle of the 19th century by Na¨geli. It comprises unicellular morphotypes with oval or cylindrical cells arranged irregularly in amorphous mucilaginous colonies. Up to now, more than 80 morphospecies have been described, mostly from various freshwater aquatic habitats. The genus Aphanothece is heterogeneous in the traditional morphological concept as well as according to modern molecular criteria. Therefore, it must be divided into several taxonomic clusters. Generic characteristics, studied by a combination of molecular sequencing of 16S rDNA, ultrastructure, ecology and morphological variation, were investigated in selected strains and populations of type species of the traditional subgenera Aphanothece and Anathece. Distinct differences were found between both of these clusters in their position in the phylogenetic tree, ultrastructure of cells, morphology (size of cells), mucilage structure, life cycles and ecology. They must therefore be separated into two genera, according to both bacteriological and botanical criteria, and placed in different orders (Chroococcales and Synechococcales). Accordingly we describe Anathece, gen. et stat. nov., and transfer to it the type A. clathrata comb. nov. and six other species. Several other morphotypes, originally classified in the genus Aphanothece (but morphologically different from Aphanothece sensu stricto), correspond to the genera Cyanoaggregatum, Cyanogastrum, Gloeobacter, Gloeothece and Halothece. The closest relative of Anathece appears to be Cyanobium.