[2] At least five other genera, Nelumbites, Exnelumbites, Paleonelumbo, Nelumbago, and Notocyamus[3][4] are known from fossils.

Nelumbonaceae are highly modified eudicots belonging to the order Proteales, their closest living relatives being the plane trees (Platanaceae) and Proteaceae.

[5] Notocyamus from the Early Cretaceous of Brazil is the oldest known representative of the family, and displays several transitional traits between Nelumbonaceae and both the Proteaceae and Platanaceae.

[4] The APG IV system of 2016 places the family in the order Proteales, in the clade eudicots.

[6][1] The Cronquist system, of 1981, also recognized this family, but placed it in order Nymphaeales in subclass Magnoliidae in class Magnoliopsida (=dicotyledons), based on gross morphological similarities.