The invasive black rat Rattus rattus has established commensal populations in most cities of the world. Known as a reservoir of numerous zoonotic diseases, this species is considered as an urban pest and may have major consequences on human health. However, little is known about the genetic structure of urban populations, although it could help to design the scale of appropriate control strategies (at the city or at the district level). In this study, we characterize the genetic structure of R. rattus within Franceville (Republic of Gabon), an African tropical city that has undergone a recent growth, like many other cities of the developing countries. Sampling was conducted in six different districts of the city, chosen to represent variable levels of connectivity and building aggregation. Genetic structure was assessed using 16 microsatellite markers. Our results suggest the occurrence of a large population of R. rattus that is continuously distributed at the scale of the city, with no impact of urban characteristics or putative barriers on genetic differentiation. Isolation by distance analyses show that effective dispersal of R. rattus is, however, spatially limited to a few hundred meters. Regarding management strategies, our results suggest that rodent control should be envisaged at the scale of the city.