Gyrodactylus patersoni n. sp. is described from the gills of the Atlantic silverside, Menidia menidia (L.) (Atherinidae), from Kingsport, Nova Scotia, Canada. The new species is the second species of Gyrodactylus to be reported from this host and is characterized by having small hamuli with short hamuli roots, a ventral bar with anterolateral processes of moderate size and a linguiform membrane, a dorsal bar with medial notch, and a male copulatory organ with 1 large spine and 5–6 terminal spines arranged in a single arched row. Gyrodactylus patersoni n. sp. most closely resembles Gyrodactylus stephanus Mueller, 1937 described from the mummichog, Fundulus heteroclitus L., from the northeastern coast of North America. The 2 species can be differentiated by the size of the hamuli (32.5 µm vs. 40.0 µm), length of the anterolateral processes (4.5 µm vs. 8.5 µm), number of copulatory spines (5–6 vs. 6–8) and, to a lesser degree, the shape of the marginal hook in that members of Gyrodactylus patersoni n. sp. have a slightly reduced heel and a more upright shaft. The description includes 438 sequenced base pairs (bp) of the 18S gene (including the V4 region) as well as 936 bp of the ITS region (ITS-1/5.8S/ITS-2). Basic Local Alignment Search Tool (BLAST) queries for the ITS and 18S fragments returned G. stephanus as most genetically similar (97.6% and 99.1%, respectively). Gyrodactylus patersoni n. sp. is a member of the Gyrodactylus arcuatus-group, a lineage that has successfully radiated through phylogenetically diverse fishes of the northern hemisphere, most of which share a littoral marine habitat.