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We analyzed the distribution and ecological relationships in the parasitic infracommunities of four species of the genus Hypostomus: Hypostomus regani, Hypostomus strigaticeps, Hypostomus hermanni, and Hypostomus ancistroides, collected in the Batalha River, State of São Paulo, Brazil. Twenty-four parasite taxa were identified among myxozoans, monogeneans, digeneans, nematodes, and hirudineans occurring in the gills, body surface, eyes, brain, and intestine. Monogeneans presented the highest species richness. The highest parasite prevalence was observed for ectoparasites in the Hypostomus spp. analyzed. Except for Phanerothecium sp., all parasites presented an aggregate pattern of distribution. In relation to parasitic diversity, H. regani presented higher mean values of diversity indexes, while H. hermanni presented higher values for the specific richness; equitability values were the same in all fish species analyzed. Infracommunities were most differentiated from one another (p < 0.05) between H. reganni and H. ancistroides. Standard length, body mass, and sex of Hypostomus spp. were significantly correlated (positively or negatively) with at least one parasite species. This study emphasizes the importance of the Batalha River as a source of local and regional biodiversity expanding the knowledge of ecological interactions between the parasite–host relationships of Siluriformes fish. [ABSTRACT FROM AUTHOR]