This genus shares many of its characters with the genus Pseudostaurosira, yet, the following combination of characters distinguishes Nanofrustulum.
Frustules are linked by marginal spines in a face-to-face manner, forming short chains. The valve face is flat to slightly domed, circular to slightly oval, with a vertical mantle. In girdle view, frustules are rectangular. Striae are uniseriate to multiseriate, composed more than two areolae that range from round to transapically elliptical. Areolae continue below the spines.
Species within this genus have a characteristic small size that ranges from 2 - 6 µm. Copula disposition is characteristic of Nanofrustulum, in which the copula are arranged as scales in a rosette-like structure.