The aim of the present study was to evaluate the helminth fauna found in the Magellanic penguin, Spheniscus magellanicus, relating parasite population and community ecological parameters to life aspects of the host species. The study involved 237 specimens of S. magellanicus taken from the northern shore of the state of São Paulo (23° 46’ S, 45° 57’ W) and southern shore of the state of Rio de Janeiro (23° 02’ S, 44° 13’ W), Brazil. The following helminth fauna were found: the nematode Contracaecum pelagicum (core species), found in the stomach; the digenetic Cardiocephaloides physalis and the cestode Tetrabothrius lutzi (satellite species), both collected from the initial portion of the small intestine. Comparisons using the Shannon Diversity Index revealed that the parasite community in juvenile penguins is less diverse in the migratory season than the breeding season. Parasitological studies on penguins and other migratory animals provide important information on species during the time in which they remain pelagic and constitute a useful tool for the acquisition of data that is difficult to obtain through other means, thereby favoring the conservation of the species.