Golden kelp (Ecklonia radiata) is the dominant habitat forming species on Australia’s Great Southern Reef, but it is under threat from anthropogenic stressors, including climate change. Genetics play a critical role in population resilience and can be used to inform conservation efforts, yet knowledge on the underlying genetic diversity of Victorian populations is lacking. Here, we use next generation sequencing to characterise patterns of genetic diversity and structure, including utilising adaptive genetic differentiation for a large-scale restoration project in Port Phillip Bay. We assessed 3416 high-quality single nucleotide polymorphisms (SNPs) across 9 sites and including 61 putatively adaptive loci. Overall, genetic diversity was low across all sites (HO: 0.006-0.011) with evidence of inbreeding (FIS 0.05 - 0.11). Populations were highly structured, with sites closer to the mouth of the bay having higher evidence of gene flow compared to the northern back of the bay. Our results provide a valuable first step to inform golden kelp restoration programs and will expand to the remainder of the Victorian coastline to also assess capacity of adaptation to environmental conditions and identify potential options for future-proofing restoration techniques.