Mesophyletis was the first genus of the group to be described, with its type description being published in 2006. The genus was placed into the family "Eccoptarthridae", an older name sometimes used for Caridae, as the one of the genera in then subfamily Mesophyletinae by George Poinar Jr. However, in the 2006 paper, no type genus was specified in the subfamily description and a subsequent paper in 2008 specified Mesophyletis as the type genus. The subfamily Aepyceratinae was proposed in 2017 as a part of the family Nemonychidae based on perceived similarities between Aepyceratus hyperochus and the nemonychids.
