Amphora pediculus should be compared with A. indistincta and A. inariensis. Amphora indistincta is similar in size, but differs by the presence of a dorsal ridge and with each stria composed of a single areola. Amphora inariensis has a silicious flap extending from the dorsal marginal ridge and dorsal areolae with expanded ends. Amphora inariensis, however, has not been verified in North America.
Amphora copulata is larger in size, has a curved raphe and 'closed' dorsal fascia as compared to A. pediculus.