We have investigated the population genetic structure of the parasitic nematode Strongyloides ratti in wild rats. In the UK, S. ratti reproduces predominantly by mitotic parthenogenesis, with sexual forms present at a rate of less than 1%. S. ratti was found to be a prevalent parasite and substantial genetic diversity was detected. Most rats were infected with a genotypic mixture of parasites. A hierarchical analysis of the genetic variation found in S. ratti sampled across Britain and Germany showed that 73.3% was explained by variation between parasites within individual hosts and 25.3% by variation between rats within sample sites. Only a small proportion (1.4%) of the total genetic variation was attributable to genetic subdivision between sample sites, suggesting that there is substantial gene flow between these sites. Most parasites sampled were found to exist in Hardy–Weinberg equilibrium and this population genetic structure is discussed in view of the virtual absence of sexual reproduction.