Alien plant pathogens are a threat to native plants and are increasingly integrating into native plant–pathogen networks, but how these novel plant–pathogen networks are structured remains unclear. Theory predicts that novel antagonists are likely to be generalists, resulting in interaction networks with greater nestedness as well as lower modularity and specialization than native networks. We tested these predictions by quantifying associations between native plants and their native and alien pathogens using a comprehensive database of plant–fungal associations in New Zealand. We compared the host ranges of alien and native pathogens and the structure of native and alien pathogen subnetworks. As predicted, alien pathogens associated with a greater number and diversity of native plant host species than native pathogens. The alien pathogen subnetwork was more nested and connected, but less modular and less specialized than the native pathogen subnetwork, consistent with expectations for novel interactions. Alien pathogens altered the overall native plant–pathogen network structure, making the full network more connected and less specialized than the native network. Modules in the native and alien subnetworks were clustered by host phylogeny but did not show a clear signal associated with host habitat or region. Synthesis. Our study provides some of the first empirical insights into the structure of novel plant–pathogen networks and the changes that occur when alien pathogens invade a native network. Because alien pathogens interacted with more hosts than native pathogens, alien pathogens have an increased risk of adverse indirect effects, including pathogen spillover, host jumps and network destabilization.