Porcellionides pruinosus is a cosmopolitan woodlouse. It is known to exhibit patterns of geographical variation between populations, and has been suspected to consist of several very closely related species. This species was found to carry Wolbachia endosymbionts, alpha-proteobacteria which are known to modify the reproduction of their crustacean hosts by inducing cytoplasmic incompatibility or feminization. In the P. pruinosus complex, Wolbachia induced feminization, but two different patterns of infection were reported: high prevalence and presence of infected males, or low prevalence and absence of infected males. In this study we investigated nine populations described as Porcellionides pruinosus carrying different Wolbachia strains, with the aim of investigating the possibility of coevolution between symbionts and hosts. Molecular analyses were carried out on both Wolbachia DNA (wsp gene) and host mitochondrial DNA (mt LSU rDNA). We show that (1) the nine host populations exhibited a high genetic differentiation so that they have to be split into two sibling species; (2) three different Wolbachia strains were found in the host complex but were not species-specific; and (3) the pattern of infection by Wolbachia was more host-dependent than symbiont-dependent.