The first known fossils of Palaeophoberus were initially assigned to another genus; Friedrich August von Quenstedt named the species Stenochirus suevicus in 1867 based on remains collected from Aalenian-aged deposits in Reutlingen, Germany.

[3] In his establishment of the genus, Glaessner (1932) considered Palaeophoberus to be related to the extant Acanthacaris, placing both genera in the family Nephropidae.

[4] The idea that these two genera were related persisted for decades, with several subsequent authors following this classification and even proposing Acanthacaris is a descendant of Palaeophoberus.

[5][6] In 1997, phylogenetic analysis carried out by Tsudy & Babcock found that Acanthacaris was not actually related to Palaeophoberus, thus the latter genus was moved out of Neophoberinae and reassigned to the family Chilenophoberidae.

[7] Karasawa et al. (2013) later declared that Chilenophoberidae is a paraphyletic grouping, synonymizing it with Stenochiridae, and reassigning all chilenophoberid genera (including Palaeophoberus) as stenochirids.