Anthropogenic reintroductions are a commonly used conservation strategy following local extirpations. However, establishing new populations with a small number of founders can result in population bottlenecks causing reduced genetic diversity, increased inbreeding, and altered genetic structuring of sub-populations. Following large-scale extirpations due to severe overharvesting in the 19th - 20th Century, many current populations of the endemic high-arctic Svalbard reindeer subspecies, Rangifer tarandus platyrhynchus, originate from recent reintroduction programs or natural recolonisations. This study uses whole-genome shotgun sequencing of 100 reindeer to investigate the population genomic consequences of both anthropogenic reintroductions and natural recolonisation. Genetic structure analyses indicate significant genetic drift resulting from reintroductions occurred, with reintroduced populations forming two distinct genetic clusters corresponding to the two reintroductions. There was little evidence for gene flow between reintroduced and natural populations, with very high genetic divergence between a reintroduced and a naturally recolonised population only separated by ~15km. However, reintroduced populations showed no significant decrease in heterozygosity or increase in inbreeding compared to the source population, and no signature of the reintroduction event could be observed in Runs of Homozygosity (RoH) length distributions. In contrast, some naturally recolonised populations showed high inbreeding (F= >0.3), longer RoH segments, and reduced heterozygosity. These results indicate that some naturally recolonised sub-populations were likely founded by a small number of individuals, and that anthropogenic reintroductions can be more effective for establishing populations with high genetic diversity than some cases of natural recolonisation. Populations naturally recolonised from remnant populations may be particularly vulnerable to the accumulation of inbreeding and drift-load, and therefore warrant particular attention in future research. These findings have relevance for the conservation and management of other species with similar life histories where natural recolonisation from fragmented populations is expected to play a key role in population recovery, or where reintroductions are being considered.