Using network analysis, we looked for broad patterns of distribution of Monogenoidea gill parasites on Neotropical freshwater fishes within a host phylogenetic framework. We analyzed a database of Monogenoidea parasitizing fishes from Neotropical rivers, from 23 watersheds, based on species descriptions published until 2011. Host-parasite interactions were organized into five matrices grouping species at different taxonomic levels. The network of interactions between host families and parasite genera was significantly modular and revealed that each fish order has a unique composition of parasite genera. Hence, interactions between lower taxa were analyzed separately for the largest fish orders (Perciformes, Siluriformes, and Characiformes). Networks tended to be loosely connected and organized in modules. Despite the putative high host specificity of monogenoids, some have a wider host range that includes distantly related host species. Among the hosts, the clade composed by the piranhas (Serrasalmus spp. and related species, Serrasalmidae) stands out in terms of parasite richness per host species, resulting in a more connected network. The history of the lineages of each host order within Neotropical freshwaters seems to have a great influence on the extent of parasite sharing. The observed modularity was influenced by both spatial structure and phylogenetic relatedness of species. In average, 37 % of modules of networks between host species and parasite genera were associated with a particular river basin and 63 % of modules were associated with a host family. Hence, spatial structure determines the co-occurrence of host and parasite species, but their evolutionary history is the main factor defining which interactions are possible.