The clouded apollo (Parnassius mnemosyne) is a palearctic butterfly with a wide distribution across Eurasia. In recent decades, however, the species has declined in many parts of its distribution range. In Sweden, both the distribution and populations size of the clouded apollo has decreased dramatically over the past two decades, mainly due to habitat loss resulting from changes in land use practices. Today, only three geographically isolated populations remain in Sweden, as well as one captive population. While previous studies have explored the population genetics of other clouded apollo populations across Eurasia, little is known about the genetics of the remaining populations in Sweden. Here we make use of whole genome resequencing data from clouded apollo individuals collected in each of the three natural populations as well as the captive population. We apply population genetic analyses and explore mitochondrial gene data when mapping to two different reference genome assemblies, to get a better understanding of the genetic structure and levels of genetic diversity of the populations in Sweden. Our results show that the clouded apollo populations in different geographic regions harbour similar but relatively low levels of genetic diversity. We also find significant genetic differentiation between the northernmost population and the populations in southern Sweden, as well as higher levels of inbreeding in this population. Our analysis of the mitochondrial CO1 gene coupled with previously available data, shows that the remaining clouded apollo populations in Sweden correspond to two distinct mitochondrial haplogroups characteristic of different regions of Eurasia. Together with our other results, this indicates a re-colonisation of Scandinavia via two different routes after the last glacial maximum. Finally, our analyses uncover sub-population substructure in one of the remaining populations in southern Sweden. Together our results provide a first overview of the populations genetics of the clouded apollo butterfly in Sweden and explore the genetic consequences of populations size declines and fragmentation in the region. These findings were communicated to local conservation authorities and used to inform conservation strategies to protect this endangered species in Sweden.