The monogenean Pseudodactylogyrus bini parasitizes the gills of eels belonging to the genus Anguilla. Circumstantial evidence suggests that the parasite has been spread accidentally from the Pacific area (East Asia) to Europe by the intercontinental eel trade. This is based on early descriptions of the parasites from Asian regions and the lack of records of the parasites in Europe before 1977. In addition, the susceptibility of European eels to infections with the parasite is significantly higher compared to that of Japanese eels, which could indicate that the European eel had not undergone co-evolution with this parasite. The present study was undertaken to elucidate the origin of the parasite by using molecular tools. Parasite samples were obtained from Europe (Germany), Asia (Taiwan) and Nova Scotia, the latter of which is the first record of P. bini in Canada. Sequencing of rDNA comprising part of the internal transcribed spacer 1 (ITS1) gene, 5.8S and part of ITS2 (1323 bp) showed that P. bini isolates from the first two regions showed high variability. One sequence was found both in a number of Asian parasites and with one to a few transitions in European parasites, which could indicate that they were split recently into the two regions. Other sequence variations suggested that one or a few genotypes of P. bini were imported on one occasion from Asia to Europe and that the two geographic isolates subsequently developed differently in the two regions. The Nova Scotian/Canadian isolates showed no variation and were found to be unique compared to the European and Taiwanese forms, indicating that this population is independent in origin. This could indicate that the Canadian parasites were introduced to North America on another occasion and independently of the European colonization.