Introduction: The persistence of generalists and specialists is a topical question in community ecology and results from both ecological and evolutionary processes. At fine taxonomical scales, ecological specialisation, i.e. organisms preferentially exploiting a subset of available habitats, is thought to be a driver promoting niche diversity. It is not clear, however, how different mechanisms interact to shape specialist-generalist coexistence. Methods: We reconstruct the structure of five bacteria-phage networks from soil isolates, and perform an analysis of the relationships between host phylogenetic diversity, parasite specialism, and parasite performance. Results: We show that the co-occurrence of species on a continuum of specialism/generalism is influenced by niche overlap, phage impact on bacterial hosts, and host phylogenetic structure. In addition, using a null-model analysis we show that infection strategies of the phages have more explanatory power than bacterial defenses on key structural features of these antagonistic communities. Conclusions: We report that generalists have more impact on their hosts than specialists, even when the phylogenetic heterogeneity of hosts is controlled for. We discuss our results in the light of their implications for the evolution of biotic interactions.