Natural habitats are increasing fragmented by human activities. This divides plants into smaller, more isolated populations. While empirical studies have shown that reductions in host population size are associated with decreasing incidence, prevalence, and severity of disease, theoretical work suggests that the presence and magnitude of this effect depends on the spatial structure of the plant-pathogen dynamic which in turn is determined by the dispersion of hosts and the dispersal of the pathogen. We have combined theoretical and empirical approaches to investigate the effects of changes in the density and size of populations of a host-plant, Podophyllum peltatum, on the abundance on a specialist, dispersal-limited plant pathogen, Puccinia podophyii. Since the variation in disease abundance among host populations emerges from intra-population processes, we estimate transmission and population growth parameters in the field and incorporate this information into a spatial mathematical model of disease transmission. This model is used to make predictions of the effects of host population size on disease abundance which are then tested against the disease abundance among host populations in twenty different forest fragments. The model's predictions that the decreasing size and density of host populations is associated with decreased prevalence and severity of disease are generally met by our field data. Given that specialist-pathogens can play important ecological roles limiting the abundance of their hosts, this work suggests that this role is diminished by anthropogenic habitat fragmentation.