A second possible species, named H. bocquentini, has been described from the Solimões Formation in Acre, Brazil, and can be distinguished from H. cruxenti by the asymmetry seen in the anterior portion of the nasals and the small distance between alveoli.

[3] Although considered a South American gryposuchine, Hesperogavialis may actually have had closer relations to the extant Gavialis known from Asia.

This has been concluded on the basis of a lack of a nasal-premaxillary contact on the rostrum that can be seen in the extinct South American gavialoids.

The position of these bones bears a closer resemblance to Gavialis by being rather slender and extending from the orbits to the middle of the rostrum while being considerably separated from the premaxilla.

It has also been proposed that this is just an independently derived characteristic unique to Hesperogavialis among the gryposuchines, and that it does not suggest any relationship to Asian gavialoids.