Recent studies have shown a phylogenetic signal in the structure of ecological networks, making the point that evolutionary history is important in explaining network architecture. However, this previous work has focused on either antagonistic (i.e., predator-prey) or mutualistic networks and has used different methodologies. Thus, a comparative assessment of both the frequency and the strength of phylogenetic signal across network types and components of network structure has been precluded. Here, we address this issue using a data set comprising 60 antagonistic and mutualistic networks. By quantifying simultaneously the matching and centrality components of network architecture-capturing the modular and nested structure, respectively-we test the presence and quantify the strength of phylogenetic signal across network types, species sets, and components of network structure. We find contrasting differences across such groups. First, phylogenetic signal is stronger in antagonistic webs than in mutualistic webs. Second, resources are more strongly constrained than consumers in food webs, while animals show more constraints than plants in mutualistic networks. Third, phylogenetic constraints are stronger for the matching component than for the centrality component of network structure. These results can shed light on the contrasting evolutionary constraints shaping network structure across interaction types and species sets.