Five levels of disease expression were scored in a cross-inoculation study of 120 host and 60 pathogen lines of wild flax Linum marginale and its rust fungus Melampsora lini sampled from six natural populations. Patterns of partial resistance showed clear evidence of gene-for-gene interactions, with particular levels of partial resistance occurring in specific host–pathogen combinations. Sympatric and putatively more highly coevolved host–pathogen combinations had a lower frequency of partial resistance types relative to allopatric combinations. Sympatric host–pathogen combinations also showed a lower diversity of resistance responses, but there was a trend toward a greater fraction of this variance being determined by pathogen-genotype × host-genotype interactions. In this system, there was no evidence that partial resistances slow host–pathogen coevolution. The analyses show that if variation is generated by among population host or pathogen dispersal, then coevolution occurs largely by pathogens overcoming the partial resistances that are generated.