The ecological mechanisms that pathogens use to exploit resources provided by hosts is an important feature that has been neglected in preference for genetic explanations underlying disease. We used a high throughput sequencing approach to determine whether ecological mechanisms for host use across four habitat types corresponded to genetic differences among three plant virus species. Genetic similarity between any of the three viruses did not correspond to similarities in host use. The most genetically distant species did share ecological strategies for host use that included a broad host range and similar occurrence patterns across the four habitats. Differences in the host community of the four habitats represented barriers to gene flow, and each virus had a particular strategy for cross-habitat colonisation. These differences might hold the key to the prediction of disease events.