We used nestedness analysis to seek non-random patterns in the structure of component communities of metazoan parasites collected from 31 sympatric fish species from the northeastern Bothnian Bay, the most oligohaline area of the Baltic Sea. Only 8 marine parasite species were found among the 63 species recorded, although some marine fish species reproduce in the bay and others occasionally visit the area. Marine parasite species can utilize both freshwater and marine fish species as intermediate or final hosts, and marine fish can harbour freshwater parasite species. This exchange of parasite species between marine and freshwater fish has probably resulted from ecological factors acting over short time scales rather than from evolutionary processes acting over longer time; the key factor probably being the immediate presence of suitable intermediate and definitive hosts. Marine fish were expected to harbour species-poor parasite communities consisting mainly of generalists acquired from the sympatric freshwater fish species, which would result in a nested pattern among the different component communities. However, an anti-nested pattern was found in the component communities of metazoan parasites of fishes from the Bothnian Bay. A likely explanation for the observed pattern is that there are specialist parasite species, the majority of which are cestodes, in some of the freshwater fish species which otherwise have depauperate parasite communities.