Hosts and parasites interact with each other in a variety of ways, and this diversity of interactions is reflected in the networks they form. To test for differences in interaction patterns of ecto- and endoparasites we analysed subnetworks formed by each kind of parasites and their host fish species in fish–parasite networks for 22 localities. We assessed the proportion of parasite species per host species, the relationship between parasite fauna composition and host taxonomy, connectance, nestedness and modularity of each subnetwork (n = 44). Furthermore, we evaluated the similarity in host species composition among modules in ecto- and endoparasite subnetworks. We found several differences between subnetworks of fish ecto- and endoparasites. The association with a higher number of host species observed among endoparasites resulted in higher connectance and nestedness, and lower values of modularity in their subnetworks than in those of ectoparasites. Taxonomically related host species tended to share ecto- or endoparasites with the same interaction intensity, but the species composition of hosts tended to differ between modules formed by ecto- and endoparasites. Our results suggest that different evolutionary and ecological processes are responsible for organizing the networks formed by ecto- and endoparasites and fish.