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Invasive species have been known to proliferate from very small invasion events containing very few individuals. This highlights the importance of stopping the spread of invasive species early, before their populations become too large and difficult to eradicate. The Reeves’ muntjac deer, native to China, has been spotted in the wild in several parts of continental Europe, including Belgium. Given the muntjac’s long history as an invasive species in the UK, and the data on the negative impacts of this species on its host environment, governments are concerned with understanding the current status of invasive muntjac and knowing the factors driving their spread. The genetic material of muntjac taken from both captive and feral populations in Flanders, The Netherlands, and the UK was assessed via Genotyping-By-Sequencing (GBS). The reduced-representation genomes were subsequently used in SNP discovery, yielding a total of 18,762 SNPs. Tests of genetic differentiation, population structure, and relatedness were run on this panel of SNPs. Pairwise FST was relatively high for populations segregated by municipality, suggesting populations were distinct from one another. Relatedness measures indicated that many of the individuals within each population had close familial relationships, partially explanatory of the significant pairwise FST values. DAPC and STRUCTURE analysis generated clusters of individuals, some of which showed consistency with expected patterns of natural dispersal, others being eclectic in composition. Relatedness measures between individuals showed strong genetic ties between captive and feral populations of muntjac. Additionally, close familial relationships revealed between individuals collected in geographically distant regions is suggestive of human-mediated translocation of muntjac. Finally, some patterns of relatedness in a geographic context suggest captive populations as the source of spreading invasive populations. These findings highlight the clear role that private keepers of muntjac have had in facilitating the spread of invasive muntjac and reinforces the value of laws restricting ownership of these animals, as even relatively small captive populations have the ability to become invasion hotspots.