In the face of an increasing number of species being threatened by extinction, museum collections can constitute a powerful resource for acquiring genomic data of endangered taxa. By utilising datasets that combine genomes from present-day populations with those from historical timepoints, several questions relevant for conservation can be investigated. In this thesis, I made use of museum specimens by combining historical and modern genomes to shed light on the genomic status of four species of conservation concern. The thesis focuses on change in genome diversity, inbreeding, and mutational load, but also divergence and structure of extinct populations and present-day populations from which sampling is difficult. Since the 1920’s, the now extinct Sumatran rhinoceros (Dicerorhinus sumatrensis) population on the Malay Peninsula likely experienced genomic erosion (chapter I). Inbreeding increased almost four-fold, and was possibly accompanied by inbreeding depression causing premature deaths and/or lowered reproductive success. Mutational load was higher in the only two remaining populations on Borneo and Sumatra, but as genomic diversity was also relatively high, a large portion of the species’ evolutionary potential might be retained if population sizes can recover quickly. The extinct New Zealand mainland kākāpō (Strigops habroptilus) population comprised higher genomic diversity and lower inbreeding, but higher mutational load, compared to the only extant population on Stewart Island (chapter II). Demographic reconstruction revealed a continuous population decline on Stewart Island since the population split between the mainland and Stewart Island populations around 10,000 years ago, and simulations demonstrated that this could have facilitated a higher efficacy of purifying selection on Stewart Island. While the arctic fox (Vulpes lagopus) is of least concern worldwide, the peripheral Scandinavian population has been threatened by extinction since the early 1900’s. A substantial increase in inbreeding was found in all Scandinavian subpopulations, but was most pronounced in southern Scandinavia (chapter III). In spite of ongoing inbreeding in the past century, genomic diversity remained stable in central and northern Scandinavia, possibly owing to post-bottleneck gene flow from Russia. The population bottleneck of a single breeding pair in the Chatham Island black robin (Petroica traversi) caused a four-fold increase in inbreeding and halved genomic diversity, but caused only minor changes in mutational load (chapter IV). In the light of population history, this suggests that prolonged periods of small population size have facilitated possibilities for purging of genetic load already prior to the historical decline. Overall, this thesis highlights not only the extensive genomic impact that anthropogenic-driven declines have had on genomic diversity of endangered animals, but also that the effect on mutational load varies between taxa.