While originally distinguished based on the presence of fontanelles on the plastron, the feature was later identified on T. hugii and E. ignoratum was designated a junior synonym.

[1] The second valid species of Thalassemys is T. marina, named in 1903 by Fraas for a partial carapace and half a plastron from the late Kimmeridgian deposits of Schnaitheim, Germany.

In 2003, it was suggested that T. marina was a synonym of the related turtle Palaeomedusa, which was based on an unknown but restored region of the original carapace.

Further assessment of the material by Anquetin and colleagues in 2017 concluded that T. moseri was distinct from the species J. oleronensis named for the skull, but was representative of the same genus.

[1] Thalassemys bruntrutana was described in 2015 by Püntener and colleagues for an almost complete carapace and plastron from a lower member of the Reunchenette Formation than other species, with referred material also from the British Kimmeridge Clay of the Isle of Purbeck.