[3] The following cladogram for the suborder Aspleniineae (as eupolypods II), based on Lehtonen (2011),[8] and Rothfels & al. (2012),[9] shows a likely phylogenetic relationship between the Thelypteridaceae and the other families of the clade.

Cystopteridaceae Rhachidosoraceae Diplaziopsidaceae Aspleniaceae Hemidictyaceae Thelypteridaceae Woodsiaceae Onocleaceae Blechnaceae Athyriaceae The family can be divided into two major clades, which the Pteridophyte Phylogeny Group classification of 2016 (PPG I) recognizes as two subfamilies, Phegopteridoideae and Thelypteroideae.

[10] The family includes several complexes of species that are difficult to distinguish, and seem to represent a remarkable evolutionary radiation.

[10] An intermediate position is to place the bulk in Thelypteris (which can then be divided into subgenera and sections corresponding to the genera of other authors) but to separate out Phegopteris and Macrothelypteris.

[5] Phylogeny of Thelypteriaceae[11][12] Macrothelypteris Phegopteris Pseudophegopteris Thelypteris Coryphopteris Metathelypteris Amauropelta Oreopteris Steiropteris Cyclogramma Stegnogramma Leptogramma Steiropteris species-group 2 Goniopteris Cyclosorus Ampelopteris Mesophlebion Meniscium Pelazoneuron Pakau Pelazoneuron species-group 2 Glaphyropteridopsis Chingia Plesioneuron Menisciopsis Grypothrix Mesopteris Plesioneuron archboldiae Strophocaulon Pneumatopteris Reholttumia Pronephrium Sphaerostephanos Trigonospora Pseudocyclosorus Amblovenatum Sphaerostephanos elatus Abacopteris Christella The Pteridophyte Phylogeny Group classification of 2016 (PPG I) accepts 30 genera:[3] Some species of Pronephrium were split off into other genera in 2021 as a result of a phylogenetic study of the family Thelypteridaceae:[15][16] The extinct genus Holttumopteris from the Cenomanian aged Burmese amber has been suggested to have affinities with the family, but several important diagnostic characters are not preserved.