Migratory hosts are key vectors of long-distance parasite dispersal. In the North Atlantic, migratory connectivity of avian hosts suggests that diplostomid trematodes with broad host specificity could potentially exhibit widespread distributions. However, host migration does not necessarily result in successful parasite dispersal. We investigated the diversity and distribution of Diplostomum spp. infecting freshwater salmonids in Greenland and the Faroe Islands using a metabarcoding approach. In Greenland, infection prevalence in Arctic char and Atlantic salmon ranged from 0% to 100% across locations. Molecular analysis revealed four lineages, including the first records of Diplostomum sp. 6, 7, and 9 (Locke et al. 2010a; 2010b), and a novel lineage/species showing 92.6–94.2% sequence identity to its closest relatives. In contrast, no evidence of diplostomid infection was found in brown trout and Atlantic salmon collected from sixteen streams in the Faroe Islands. The presence of a novel, locally abundant (28.9% prevalence) parasite lineage/species in Greenland, the affinity of these parasite assemblages with those in North America, the lack of overlap with Icelandic and Norwegian communities, and the absence of diplostomids in Faroese salmonids indicate limited bird-mediated dispersal of diplostomids across the North Atlantic. We propose that a ‘short transmission window’ at high latitudes during the breeding season, combined with specific avian migration routes, may limit long-distance dispersal and promote regional isolation between Nearctic and Palearctic diplostomid communities across the North Atlantic.