Megalobatrachonema nipponicum Yamaguti, 1941 (Nematoda: Cosmocercoidea: Kathlaniidae), the type species of the genus Megalobatrachonema, had been only once reported from the Japanese giant salamander, Andrias japonicus (Temminck, 1836) (Amphibia: Cryptobranchidae), in the last 80 years. Herein, we reported the present species from A. japonicus and hybrids ( A. japonicus × Andrias davidianus (Blanchard, 1871)) following the original description. The examined specimens were morphologically identical to the original description. We showed the phylogenetic position of M. nipponicum among cosmocercoid species as well as among congeneric species, which suggested the polyphyly of the genus. In addition, the phylogenetic analysis did not support the subgenera in this genus. Thus, we considered the presence or absence of an esophageal bulb valve as a key morph to identify species, not subgenus, of Megalobatrachonema.
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