Abstract Assessing the genetic diversity and gene flow among populations in combination with ecological data provides valuable insight into the spatial use and genetic structure of wildlife. Anthropic impact generates landscape changes that threaten species by favouring their isolation in small patches and limiting their connectivity. However, in some cases, it can increase genetic exchange among wild populations. Here, we used a set of 16 microsatellites to study the genetic diversity, population genetic structure, and historical and current gene flow of coypu (Myocastor coypus) populations, a semi-aquatic rodent that inhabits watercourses of the highly anthropized agroecosystems of the Pampas region. Our results showed moderate to high levels of genetic diversity and revealed the existence of genetic structure among populations. Bayesian analysis showed different patterns of genetic structure among and within sampling sites. Also, the patterns of historical gene flow differed from that seen today. These results, together with previous studies, suggest that anthropic pressure, habitat fragmentation and ephemeral landscapes in a highly modified ecosystem could alter the dispersal patterns of coypus in their native range, which would otherwise be different in an environment with low anthropic impact. The results provide new information that could be used in effective conservation programmes.