Fundulotrema porterensis n. sp. (Monogenea: Gyrodactylidae) is described from the mummichog, Fundulus heteroclitus (L.; Cyprinodontidae), inhabiting Porters Lake, Nova Scotia, Canada. The new parasite species is characterized by having a ventral bar with small anterolateral processes and linguiform membrane, differentiating it from all other known species of Fundulotrema. The morphological description of F. porterensis is supplemented with 1,011 sequenced base pairs (bp) of ribosomal DNA (rDNA) spanning both internal transcribed spacers (ITS-1 and ITS-2) and 5.8S regions of the genome. A BLAST (basic local alignment search tool) search revealed that the 5.8S (157 bp) region varied by 1 bp from Gyrodactylus turnbulli Harris, 1986 and G. pictae Cable, Oosterhout, Barson and Harris, 2005, which also infect cyprinodontids. Morphometrically, F. porterensis most closely resembles Fundulotrema foxi (Rawson, 1973), but the 2 species are easily separated by length of hamuli (50.7 vs. 42.2 µm, respectively), length of anterolateral process of the ventral bar (4.9 vs. 8.9 µm), shape of marginal hooks, and shape of the ventral bar membrane. A morphological and molecular supplemental diagnosis of Gyrodactylus stephanus Mueller, 1937, from the mummichog, is also presented. This new material provides previously unrecorded information on the attributes of the ventral bar, marginal hooks, and also clarifies the structure of the male copulatory organ (MCO).