Bassipterus is classified as part of the family Adelophthalmidae, the only clade ("group") within the superfamily Adelophthalmoidea.
It was originally described as a hughmilleriid, but since then it has been considered closer to Adelophthalmus than to Hughmilleria.

Bassipterus and Pittsfordipterus form a basal ("primitive") group that differentiate them from the other adelophthalmids.
This clade is backed by a pair of synapomorphies (shared characteristics different from that of their latest common ancestor); relatively long and narrow eyes and a complex termination of the genital appendage.
Therefore, Pittsfordipterus is the sister group (closest relative) of Bassipterus.
Bassipterus was also similar to Parahughmilleria, a derived adelophthalmid whose metastoma, telson and body were slightly differentiated.
This has led some authors to synonymize Bassipterus with Parahughmilleria, though this is not currently supported.

The cladogram below presents the inferred phylogenetic positions of most of the genera included in the three most derived superfamilies of the Diploperculata infraorder of eurypterids (Adelophthalmoidea, Pterygotioidea and the waeringopteroids), as inferred by Odd Erik Tetlie and Markus Poschmann in 2008, based on the results of a 2008 analysis specifically pertaining to the Adelophthalmoidea and a preceding 2004 analysis.
Bassipterus is classified as part of the family Adelophthalmidae, the only clade ("group") within the superfamily Adelophthalmoidea. It was originally described as a hughmilleriid, but since then it has been considered closer to Adelophthalmus than to Hughmilleria.
Bassipterus and Pittsfordipterus form a basal ("primitive") group that differentiate them from the other adelophthalmids. This clade is backed by a pair of synapomorphies (shared characteristics different from that of their latest common ancestor); relatively long and narrow eyes and a complex termination of the genital appendage. Therefore, Pittsfordipterus is the sister group (closest relative) of Bassipterus. Bassipterus was also similar to Parahughmilleria, a derived adelophthalmid whose metastoma, telson and body were slightly differentiated. This has led some authors to synonymize Bassipterus with Parahughmilleria, though this is not currently supported.
The cladogram below presents the inferred phylogenetic positions of most of the genera included in the three most derived superfamilies of the Diploperculata infraorder of eurypterids (Adelophthalmoidea, Pterygotioidea and the waeringopteroids), as inferred by Odd Erik Tetlie and Markus Poschmann in 2008, based on the results of a 2008 analysis specifically pertaining to the Adelophthalmoidea and a preceding 2004 analysis.
Bassipterus