1. A long-term study (19 years) of a host–pathogen metapopulation involving 133–220 separate populations of the wild plant Filipendula ulmaria and its rust pathogen Triphragmium ulmariae shows marked changes in the occurrence (32–55% demes) and severity of disease and rates of extinction and re-establishment of individual populations (0.006–0.174 and 0.030–0.195 per annum, respectively) over time.
2. Modelling of the spatio-temporal dynamics of disease demonstrated year-to-year changes associated with a range of different environmental features, but also more consistent, longer-term patterns influenced by a complex suite of factors.
3. Both the level of disease and its spatial location varied through time and generated a changing pattern of selective pressure across the metapopulation.
4. Synthesis. Our results suggest that co-evolutionary hot spots and cold spots can be highly dynamic within metapopulations, thereby fuelling the co-evolutionary process even more than previously suspected.