The earliest discovered specimens of J. spinulatus were assigned by Heinrich Balss to the species Stenopus spinosus. Its first description as a separate species was the type description by Lipke Holthuis in 1946, where it was given the name Engystenopus spinulatus. This was based on a single damaged holotype male, collected in the Lobetoli Strait, east of Flores, Indonesia, and the placement in the genus Engystenopus was considered questionable. The most distinctive characteristics of Engystenopus are characters of the third pereiopod, which was lacking from all the early specimens. When specimens with intact third pereiopods became available, Joseph Goy realised that "E. spinulatus" did not belong in the same genus as E. palmipes (the only other species of Engystenopus), and erected a new genus, Juxtastenopus, to hold it. The two genera are now placed in different families, although both names carry the meaning "close to Stenopus"; Engystenopus is one of seven extant genera in the family Spongicolidae, while Juxtastenopus is one of four extant genera in the family Stenopodidae.
