The Megapodagrionidae are usually divided into five or six subfamilies:Argiolestinae Hypolestinae Megapodagrioninae Philosininae Pseudolestinae (often treated as distinct family)
In addition, two monotypic genera are sometimes placed here as monotypic subfamilies: Thaumatoneura is otherwise regarded as a monotypic family of the Calopterygoidea. Coryphagrion was usually also considered a monotypic family in older treatments; in recent times it is often included in the Pseudostigmatidae of the superfamily Coenagrionoidea. The extinct genus Electropodagrion was described from a fossil in Baltic amber in 2008 and placed into the family, with no subfamily designation.
A 2013 phylogenetic analysis pares down this family into only three genera:Allopodagrion Megapodagrion Teinopodagrion