Surirella atomus is smaller than most other species of Surirella, with a width of 5-8 μm. Surirella atomus is easily confused with S. stalagma, but S. atomus lacks a capitate footpole and apical line. In addition, the headpole of S. stalagma is more narrow. Surirella atomus is distinguished from S. suecica by its broader fibulae.