[2][3] Although lungfish originated in marine environments, the Ceratodontiformes have been an exclusively freshwater group since the Carboniferous.

[5] The suborder was formerly defined as being within the order Ceratodontiformes and including the families Neoceratodontidae and Ceratodontidae, as they were formerly thought to be closely related to one another.

[citation needed] However, phylogenetic analyses indicate that this classification is paraphyletic, as Ceratodontidae was found to be a sister group to a clade containing Lepidosirenidae, which was formerly classified as Lepidosireniformes, a distinct order from Ceratodontiformes.

[7] Kemp et al (2017) found the following taxonomy based on morphological evidence: †Paraceratodus †Ferganoceratodus Neoceratodontidae Lepidosirenidae Protopteridae †Gnathorhizidae †Ptychoceratodontidae †Ceratodontidae Based on this treatment, the oldest fossils of the Ceratodontiformes are of Gnathorhizidae from the Late Carboniferous, which are thought to be closely related to modern Lepidosirenidae and Protopteridae.

This would indicate that the order itself originated slightly earlier in the late Carboniferous and rapidly diversified into the multiple families between then and the start of the Permian, leading to a very deep split between the Neoceratodontidae and the Lepidosirenidae + Protopteridae.