Pterygotus is classified within the family Pterygotidae in the superfamily Pterygotioidea, lending its name to both its family and its superfamily.
The three most derived pterygotid eurypterids, Acutiramus, Jaekelopterus and Pterygotus, are very similar to each other.
Pterygotus is particularly similar to Jaekelopterus, from which it is virtually only distinct in features of the genital appendage and potentially the telson.

Similarities in the genital appendage could mean that the three genera are all synonyms of each other, as they had been classified in the past (as species of Pterygotus).
Some differences between them have also been noted in the chelicerae, though chelicerae have been questioned as the basis of eurypterid generic distinction since their morphology depends on the lifestyles and has been observed to vary throughout ontogeny.
Telson morphology is sometimes used as a distinguishing feature, though the telsons of the three derived pterygotid genera are all paddle-shaped (the telson of Jaekelopterus is triangular, but might fall into the morphological range of the other genera).
An inclusive phylogenetic analysis with multiple species of Acutiramus, Pterygotus and Jaekelopterus is required to resolve whether or not the genera are synonyms of each other.

The cladogram below is based on the nine best-known pterygotid species and two outgroup taxa (Slimonia acuminata and Hughmilleria socialis).
The cladogram also contains the maximum sizes reached by the species in question, which have been suggested to possibly have been an evolutionary trait of the group per Cope’s Rule ("phyletic gigantism").
Pterygotus is classified within the family Pterygotidae in the superfamily Pterygotioidea, lending its name to both its family and its superfamily. The three most derived pterygotid eurypterids, Acutiramus, Jaekelopterus and Pterygotus, are very similar to each other. Pterygotus is particularly similar to Jaekelopterus, from which it is virtually only distinct in features of the genital appendage and potentially the telson.
Similarities in the genital appendage could mean that the three genera are all synonyms of each other, as they had been classified in the past (as species of Pterygotus). Some differences between them have also been noted in the chelicerae, though chelicerae have been questioned as the basis of eurypterid generic distinction since their morphology depends on the lifestyles and has been observed to vary throughout ontogeny. Telson morphology is sometimes used as a distinguishing feature, though the telsons of the three derived pterygotid genera are all paddle-shaped (the telson of Jaekelopterus is triangular, but might fall into the morphological range of the other genera). An inclusive phylogenetic analysis with multiple species of Acutiramus, Pterygotus and Jaekelopterus is required to resolve whether or not the genera are synonyms of each other.
The cladogram below is based on the nine best-known pterygotid species and two outgroup taxa (Slimonia acuminata and Hughmilleria socialis). The cladogram also contains the maximum sizes reached by the species in question, which have been suggested to possibly have been an evolutionary trait of the group per Cope’s Rule ("phyletic gigantism").
Pterygotus