It is known from a single holotype incomplete, partially disarticulated skull and left lower jaw called PEFO 34034 from the Upper Lot's Wife beds, Sonsela Member of the Chinle Formation in Petrified Forest National Park.

Many characteristics that associate Protome with other phytosaurs can be found in its squamosal bone, which makes up the cheek region and extends behind the main portion of the skull.

A third autapomorphy is a small depression or fossa surrounding the front tip of a hole in the lower jaw called the mandibular fenestra.

Protome and Leptosuchus are similar in that both have broad squamosals and holes called supratemporal fenestrae that are located on top of the skull.

As was the case in previous studies, species of Leptosuchus formed a paraphyletic grouping, meaning that they did not represent one coherent genus.