Both the generic and the specific name refer to the Mokle-mbmb, a water-dwelling mythological creature from Central Africa, generally associated with a reptilian form, and usually characterized by the presence of a relatively long neck, this being a common character for Pleurodira.

Mokelemys mbembe was named by Pérez-García (2022). Its type specimen is MRAC rt15_eg_01, a partial skull, and it is a 3D body fossil. Its type locality is Sinda-Mohari crocodilians, which is in a Pliocene terrestrial horizon in the Sinda Beds Formation of the Congo-Kinshasa. It is the type species of Mokelemys.