Calicotyle japonica n. sp., collected from the uterus, rectal gland, archinephric duct and cloaca of the shortspine spurdog Squalus mitsukurii Jordan & Snyder (Squaliformes) off the Pacific coast of Japan, is described. The new species can be distinguished from C. inermis Woolcock, 1936 by the shape of the male copulatory organ; in C. japonica this is directed anteriorly, is sharply bent in the middle and then increases in width toward the tip, whereas it is long, coiled and uniform in width throughout its entire length in C. inermis. Furthermore, the intestinal caeca have many irregular diverticula on both sides and the vaginal apertures are at the level of the common genital pore in C. japonica, whereas in C. inermis the intestine is smooth and the vaginae open at the level of the oötype. A phylogeny constructed using LSU rDNA data indicates that the new species is grouped with other Calicotyle species; based on this, Gymnocalicotyle Nybelin, 1941 is synonymised with Calicotyle Diesing, 1850. Calicotyle is divided into two major clades, with the new species being grouped with Calicotyle species infecting sharks and the second clade consisting of Calicotyle spp. infecting rays. This suggests that the loss of the hamuli in C. japonica and C. inermis, both parasites of sharks, is a comparatively recent event in the evolution of the genus.