Few studies have investigated the genetic structure of both host and parasite populations at a level of populations and at a level of individuals. We investigated the genetic structure of the urban cockroach Blattella germanica and its oxyuroid parasite Blatticola blattae. Random amplified polymorphic DNA (RAPD) markers were used to quantify genetic diversity between and within four populations (from two cities in France) of the host and its parasite. Diversity based on phenotypic frequencies was calculated for each RAPD marker using Shannon-Wiener’s index. We used multivariate analyses to test the significance of genetic differentiation between host and parasite populations. Analysis of molecular variance was also used. Both methods gave similar results. Diversity between pairs of individuals was estimated by Nei & Li’s index. Genetic diversity was higher within host or parasite populations (80% and 82%, respectively, of explained diversity) than between host or parasite populations (20% and 18%, respectively, explained diversity). The genetic distances between pairs of parasite populations (or individuals) were not correlated with the genetic distances between the corresponding pairs of host populations (or individuals).