The genus was named in 2002 by Alexander Kellner and Diogenes de Almeida Campos. The type species is Thalassodromeus sethi. The genus name is derived from Greek thalasse, "sea" and dromaios, "runner", in reference to its presumed life style as a skimmer. The specific name refers to the Egyptian god Seth because of the similarity in head form. In 2006 André Jacques Veldmeijer suggested Kellner had confused Seth with the god Amun whose crown shows a remarkable resemblance with the Thalassodromeus head crest.