The grey partridge population has experienced significant declines across Europe, largely due to agricultural intensification and loss of habitat, leading to conservation actions such as Red-listing in the UK and hunting bans in Greece. The genetics of Balkan and Scottish populations remain largely unexplored; genetic analyses are essential to evaluate the impact of past restocking efforts on wild populations, as breeding between released and wild-living partridges may complicate recovery efforts. In this study, we sample wild and farmed individuals of grey partridge from the Balkans (Greece, North Macedonia) and the United Kingdom (UK) and employ 2300 SNPs, eight microsatellites and two mitochondrial markers to investigate the genetic structure and diversity of their populations and the impact of past restocking activities. We reveal a clear distinction between two clades, an Eastern and a Western, as in previous studies, with wild birds from Greece and the UK classified to each clade respectively. However, birds from North Macedonia belonged to either clade, suggesting a contact zone between the two or a genetic legacy of past restocking practices. The captive stock in Greece and the UK is clearly of Western origin, with minor introgression of the Eastern clade being detected. Finally, an informative SNP marker panel is presented that accurately assigns each individual to either the Eastern or Western clade and will serve as a valuable tool for monitoring population structure, guiding conservation efforts, and assessing the impact of restocking activities on grey partridge populations.