Detecting the number of invasions is crucial to understanding the process of invasion and perhaps the success of some invasive pest species. Detecting multiple invasions can be difficult using partial mitochondrial COI, however, due to lack of variation. To examine the post-invasion history of Bemisia argentifolii (also called B. tabaci Middle East-Asia Minor 1 and B biotype) in Australia and test for the presence of spatial genetic structure, we developed microsatellite loci based on the whole-genome sequence of B. argentifolii. We investigated gene flow among populations of B. argentifolii collected between 1995 and 2018, covering the time since the first detection in Australia (1994). Structure plots and PCAs of the microsatellite data revealed three clusters in 1995–1996, indicating multiple introductions. Since then, B. argentifolii has become a widespread single genetic population across the continent, with no geographic genetic structure in recent samples. The haplotype network generated from mitochondrial COI shows that Australian B. argentifolii mostly has the same haplotype as the invasive populations established elsewhere around the world. Analysis of the more recent samples showed that gene flow was high across regions, indicating movement of B. argentifolii across Australia is currently extensive. Undesirable traits and pathogens not already present in Australia, including insecticide resistance and plant viruses, could arrive with any new introductions of B. argentifolii and are likely to spread rapidly and be difficult to contain. This highlights the importance of biosecurity and continued quarantine measures to prevent new incursions, even when a species has already established.