In this paper we introduce a method to analyze the inter- and intraspecies transmission rates and contact structure between susceptible and infected plants in epidemics in mixed plant populations. Using spatiotemporal maps of damping-off epidemics caused by Rhizoctonia solani in replicated microcosms of >400 randomly mixed radish and mustard seedlings, we first show that as an epidemic progresses through a mixed plant population it changes the contact structure between infected (I) and susceptible (S) plants, so that resistant plants are challenged progressively more frequently, thereby slowing the epidemic. We estimate the transmission rates for each of the four S–I pair combinations. All transmission rates rose initially with time and then declined, with overall lower rates for the more resistant mustard species. However, the interspecies transmission rates were unexpectedly high. We show how these rates relate to relative changes in infectivity and susceptibility of each host species, and how a species that is weakly susceptible in a pure stand can still act as a strong donor of disease in a mixture, thereby lowering the efficacy of the mixture to reduce disease. We discuss the broader consequences for the dynamics of disease in natural and managed populations.