Gyrodactylus leptorhynchi n. sp. (Monogenea) is described from bay pipefish (Syngnathus leptorhynchus) (Syngnathidae) in coastal waters of southern California and British Columbia, and from an outbreak of gyrodactylosis at the Cabrillo Marine Aquarium in California. Gyrodactylus leptorhynchi is morphologically similar (stout hamuli, superficial bar with no anterolateral processes, and a small, triangular membrane, similarly shaped marginal hook sickles, and a male copulatory organ [MCO] with numerous small spines) to the other 6 species of Gyrodactylus known from pipefish in north and south regions of the Atlantic Ocean. It resembles most closely Gyrodactylus corleonis Paladini, Cable, Fioravanti, Faria, and Shinn, 2010, parasitizing Syngnathus typhle L. from the French Mediterranean in having relatively large hamuli (58 μm). However, in G. leptorhynchi, the marginal hook sickle has a reduced heel and a ledged toe, while in G. corleonis, it has a noticeable heel and a toe with no distinct ledge. DNA sequence data of a partial ITS1 (700+ bp), complete 5.8S (157 bp), complete ITS2 (392 bp), and a partial 18S (441 bp) are included in the description; the data are distinct from those available for other species of Gyrodactylus. The molecular data reveal that G. leptorhynchi is a member of a basal lineage of marine species within Gyrodactylus sensu lato that is known to have radiated among coastal syngnathid, anguillid, and gobiid fishes throughout the Atlantic Ocean and some adjacent waters. Occurrence of G. leptorhynchi in the eastern Pacific supports the idea that such lineages may have global distributions. Sixty-three percent (15 of 24) of bay pipefish caught at Inner Cabrillo Beach, California, were infected with 1–3 worms, predominately located on the dorsal fin, but also on the anterior body surfaces. Intensely infected pipefish at the marine aquarium had parasites distributed all over the body surface, including the open edge of the brood pouch and, on 2 occasions, inside the brood pouch. A quarantine protocol, involving the treatment of wild pipefish with serial repeats of topical anthelmintic chemicals (formalin, Trichlorfon, and Praziquantel), that helps to diminish outbreaks of G. leptorhynchi in aquarium exhibits is described.