The phylogenetic relationships of baphetids is uncertain; while many studies have placed the group as a close relative of Amniota, other analyses have found Baphetidae to be a more basal clade of early stem tetrapods.

The baphetids have been referred to the family Loxommatidae, but this group was later shown to be a junior synonym of Baphetidae, which was named earlier in 1865.

Their best-known characteristic was a curious, keyhole-shaped orbit formed by excavation of the lacrimal and prefrontal bones in front of the eye.

There is a strongly embayed spiracular ("otic") notch, but the stapes is distally broad, which seems to rule out a sensitive hearing apparatus.

The traditional four genera of baphetids (Loxomma, Baphetes, Megalocephalus, and Spathicephalus) have recently been supplemented by Eucritta, a somewhat different form.

Computer-assisted phylogenetic analyses of a data matrix using characteristics of most of the major groups of terrestrial vertebrates place the Baphetids close to the ancestry of amniotes[citation needed].