We use 14 microsatellite loci to investigate the impact of a viral disease (Ranavirus) on the population genetic structure of wild common frogs (Rana temporaria). Populations with a history of Ranavirus mortalities (and 83% declines in the number of frogs) were compared with populations with no history of infection. Infected ponds showed significantly elevated FIS (homozygote excess), significantly reduced relatedness, and no detectable effect on allelic richness. We hypothesize that the elevated FIS and reduced relatedness are consequences of assortative mating, and that allelic richness is maintained by immigration from nearby populations. Simulations indicate that the elevated FIS cannot be explained by population size reductions, but can indeed be explained by assortative mating (even if a mate choice locus is unlinked to the genetic markers). While the majority of studies consider demographic outcomes following disease outbreaks, our results indicate that emerging infectious diseases could also result in behavioural changes.