In the current study, a total of 102 common Todarodes pacificus squid caught in the East Sea were investigated for parasitological research. The results revealed that 33 (32.35%) out of 102 squid were infected by Nybelinia surmenicola, the mean intensity was 5.58 parasites per squid, and the maximum abundance was 11. Morphological analysis using a field emission scanning electron microscope showed the characteristic features of N. surmenicola. Molecular identification based on the 28S rRNA gene confirmed the isolated parasite as N. surmenicola, while phylogenetic analysis revealed that N. surmenicola isolated in this study was clustered with N. surmenicola isolated from Japan. This is the first report of phylogenetic characterization of N. surmenicola isolated from Korea.