Island biodiversity is especially vulnerable to the negative impacts of invasive species. Myriad examples over the past few decades have demonstrated the effectiveness of invasive species eradication as an effective conservation and restoration strategy on islands. Population genomics can support management planning by delineating eradication units (i.e., genetically distinct populations) and identifying potential sources of reinvasion. Here, we conducted population genomic analyses to guide the management of invasive European fallow deer (Dama dama) on Sidney Island in British Columbia, Canada. Specifically, we aimed to determine whether deer on Sidney Island were genetically isolated from deer on two nearby islands, James and Mayne, which represented potential sources of reinvasion. To that end, we genotyped 44 individuals across the three islands at 8,528 genome-wide single-nucleotide polymorphisms, revealing strong pairwise genetic differentiation, with no evidence of gene flow among islands. The contemporary population of Sidney Island also exhibited extremely low genetic diversity, likely reflecting low propagule pressure, founder effects, and/or the cumulative impacts of genetic drift due to decades of culling. Taken together, these results suggest that Sidney fallow deer are genetically isolated and that a successful eradication is unlikely to be undermined by natural reinvasion from nearby islands, providing an opportunity for ecosystem restoration. This work more broadly demonstrates the ability of population genomics to guide the management of invasive species on islands by assessing invasion history, dispersal capacity, and reinvasion risk, ultimately improving opportunities for successful and sustainable conservation outcomes.