The parasite faunas of juvenile English sole (Parophrys vetulus) in 1971–1972 and staghorn sculpin (Leptocottus armatus) in 1971 from Yaquina Bay, Oregon, were compared with faunas found in the same estuary in 1997–2000 (English sole) and 1999–2000 (staghorn sculpin). The 7 most commonly occurring parasites in 1971 were compared with the same species observed during the same month and sampling sites in 1997–2000. Multivariate community analysis of juvenile English sole parasites supported the suggestion that the 1971 parasite data were representative of the early-1970s time period. Four of the parasite species infecting English sole and 6 of those infecting staghorn sculpins had significantly lower prevalences in 1997– 2000. Parasite species with significantly lower prevalences also had reduced intensity levels. One parasite (Glugea stephani) of English sole increased in prevalence in the 1997–2000 samples in association with the warm estuarine temperatures during the 1997 El Niño year. Although the causes for the changes in occurrence of other parasites were not determined, ecological changes in Yaquina Bay that may have influenced parasite ecology include apparent changes in the estuary ichthyofauna that occurred between the sampling periods. Such changes could be associated with increases in the number of California sea lions (Zalophus californianus) subsequent to establishment of the Marine Mammal Protection Act in 1972.