Hyponeoidae is a copepod family that is rare around the world, with only three species described until now. Recently, a hyponeoid copepod was found in the narrowmouthed catshark, Schroederichthys bivius, from Chile, which has not been formally described. The objective of this study is to describe morphologically a new species of Hyponeoidae, from samples of the Strait of Magellan, Southern Chile. Also, a genetic analysis, based on the COI gene, was used to determine the relatedness of the new hyponeoid species to other copepods from Siphon-ostomatoida, which were available in the GenBank platform. The new species belongs to the genus Tautochondria and is here described as T. magellanica n. sp. This species differs from T. dolichoura mainly in the presence of long process at each side of the buccal cone, the absence of lobes on the head and short processes on the genital complex. According to the genetic sequences, T. magellanica n. sp. was not closely related to any other species. Therefore, this result confirms that Hyponeoidae is a separate family. However, the relatedness to other genera in Siphonostomatoida is still unknown.