The recently established genus Sphaerospermopsis was characterized by spherical akinetes located on one or both sides of heterocytes. The establishment of the new genus was supported by the clustering of the 16S rRNA gene. Natural populations of the genus may be overlooked when akinetes are absent. In this study, a new Sphaerospermopsis species, Sphaerospermopsis crassa, and other Sphaerospermopsis species were taxonomically evaluated by combining morphology and molecular data on the 16S rRNA gene and the 16S-23S rRNA internally transcribed spacer (ITS). New insights into the taxonomy of the genus Sphaerospermopsis were obtained. The ITS secondary structures from seven Sphaerospermopsis strains of three species showed the same pattern of D1-D1', Box-B and V3 helices, which distinguished them from other heterocytous genera. Furthermore, the V2 helix was quite variable and useful for species delimitation within Sphaerospermopsis.