Remipedia are rare and ancient mandibulate arthropods inhabiting almost inaccessible submerged cave systems. Their phylogenetic position is still enigmatic and the subject of extremely controversial debates. To contribute arguments to this discussion, we analyzed the brain of Godzilliognomus frondosus Yager, 1989 (Remipedia, Godzilliidae) and provide a detailed 3D reconstruction of its anatomy. This reconstruction yielded the surprising finding that in comparison with the brain of other crustaceans such as representatives of the Branchiopoda and Maxillopoda the brain of G. frondosus is highly organized and well differentiated. It is matched in complexity only by the brain of ''higher'' crustaceans (Malacostraca) and Hexapoda. A phylogenetic analysis limited to brain anatomy across the Mandibulata strongly contradicts the prevailing hypothesis that the Remipedia are a basal, ancestral crustacean group but instead argues in favor of a remipede-malacostracanhexapod clade and most likely a sister-group relationship of Remipedia and Malacostraca.

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