It was once thought to be a population of the West African slender-snouted crocodile (Mecistops cataphractus) but was elevated to a species after two detailed studies, one in 2014 and the other in 2018.

[5] Studies of specimens and their molecular sequences established that there were two different species which occurred in distinct hydrological zones.

M. leptorhynchus is easily differentiated morphologically from M. cataphractus by the absence of a round tubercle or boss on the squamosal scale at the back of the head in the former and present in the latter.

[3] Shirley et al. (2018) also designated M. cataphractus as the type species of Mecistops in accordance with Articles 69 and 70 of the ICZN.

M. cataphractus best serves stability because it is the most well-studied species of Mecistops with the most readily recognizable and assignable type material.