Recently two unidentified Notocotylus species have been recovered from a mallard in Hokkaido, Japan. Preliminary data indicated that one of them may belong to N. atlanticus—a species found in Europe and on the Atlantic coast of North America. Now we have sequenced partial cox1 for several European N. atlanticus isolates and performed a barcode gap analysis. It has shown the conspecificity of European and Japanese worms, bringing up discussion on distribution, transmission and host specificity in this species.