Palatodonta was first named by James M. Neenan, Nicole Klein and Torsten M. Scheyer in 2013 and the type species is Palatodonta bleekeri. The generic name refers to the row of teeth on the palatine bone of the palate. The specific name honours Remco Bleeker, an amateur paleontologist, who discovered the fossil in the summer of 2010 at the Silbeco quarry near Winterswijk.