N. californiensis was originally described in 1854 by James Dwight Dana as a member of the genus Callianassa, giving the type locality as "California"; the material Dana studied was probably collected from San Francisco Bay or Monterey, but the original specimens have since been lost. In 1991, Raymond Manning and Darryl Felder transferred the three species in that genus that come from California and Oregon into the new genus Neotrypaea. N. californiensis is distinguished from the other two species of Neotrypaea by the lack of a rostrum (which is present in Neotrypaea gigas) and the acute and diverging tips of the eyestalks (which are short, blunt and not diverging in Neotrypaea biffari).
