[1] The genus name derives from the Greek plemmyris ('tide' or 'wave') and dytes ('diver'), while the specific name honors John Shinton, a fossil preparator at the Denver Museum of Natural History where all known specimens of this taxon are reposited following collection in the late 20th century.

Huttenlocker et al. (2007) differentiated Plemmyradytes from other amphibamiforms by: (1) the reduced lateral exposure of the palatine (LEP); (2) a long and narrow supratemporal without a ventral flange; (3) a posteriorly extensive squamosal, long and slightly recurved teeth that decrease in size posteriorly; (4) a shallow dentary with a trough below the tooth row; and (5) smaller teeth on the dentary relative to the maxilla.

[2] Conversely, updated character coding resulted in P. shintoni being recovered as the sister taxon to Eoscopus.

Similarly, Fröbisch & Reisz (2008) recovered P. shintoni as being closer to amphibamids proper (Doleserpeton + Amphibamus) between the Carboniferous amphibamiforms Eoscopus from Kansas and Platyrhinops from Ohio.

Subsequent analysis with increased taxon sampling using the same matrix by Maddin et al. (2013) recovered the same results.