The larval form of the Phyllobothriidea cestode was found in the blubber of a Cape fur seal (Arctocephalus pusillus pusillus) from a zoo in Japan. Bladder-bearing larval cestodes with a scolex have been occasionally reported from blubbers of pinnipeds and morphologically identified as Clistobothrium delphini (formerly known as Phyllobothrium delphini) or rarely Clistobothrium grimaldii (Monorygma grimaldii). Although the larvae here morphologically resembled C. delphini, the 28S rDNA sequence was 100% (1,430/1,430 bp) homologous to the registered sequence of C. grimaldii (GenBank Accession No. KU724058). This discrepancy between morphological and molecular analyses confirms the difficulty of identifying C. delphini and C. grimaldii larvae based solely on morphology, and the need for molecular data to elucidate the morphological variations in Clistobothrium parasites.