Loss of genetic variation through genetic drift and inbreeding is a major threat to small and isolated populations. Although previous studies have generally used genetically verified pedigrees to document effects of inbreeding and gene flow, these often fail to capture the whole inbreeding history. Also, empirical support for a link between genomic inbreeding and fitness is scarce. By sequencing complete genomes of 23 Scandinavian arctic foxes (Vulpes lagopus) born before and after an immigration event, we here look into the genomic consequences of inbreeding and genetic rescue. We found a significant difference, with 18% higher genome-wide heterozygosity and 81% lower genomic inbreeding in immigrant F1 compared to native individuals. However, more distant descendants of immigrants (F2, F3) did not show the same pattern. We also found that foxes surviving their first year generally had higher heterozygosity and lower inbreeding than non-survivors. Finally, pedigree-based inbreeding correlated with, but underestimated, genomic inbreeding levels. Our results demonstrate a fundamental link between genetic variation and fitness, the transient nature of genetic rescue, and that inbreeding is even more severe than captured from a genetically verified pedigree. Our results have important implications in conservation biology as inbreeding depression can be detected in populations lacking a pedigree.