There is an urgent need to study inbreeding, genetic drift and mutational load in a range of natural at-risk populations that may be trapped in an extinction vortex. To date, most genomic studies have focused on species of terrestrial vertebrates and studies on aquatic mammalian key predators are currently underrepresented. The harbour porpoise (Phocoena phocoena) is a marine top predator that plays an important role in ecosystem functioning. The species colonised the Baltic some 10 000 years BP, at the end of the last glaciation. In the Baltic region, there are now three recognised populations: (i) the Belt Sea population, (ii) the North Sea population and, (iii) the Baltic Proper population, which differ from each other morphologically, genetically and in their distribution patterns. During recent decades, the Baltic Proper population has severely declined. The extant population numbers ~500 individuals and is listed as critically endangered by the IUCN and by the Baltic Marine Environment Protection Commission. Its decline is attributed to high levels of bycatch and high environmental toxin loads. Although the Baltic Proper harbour porpoise used to be common in the Baltic Sea, there is no reliable estimate of the historical population size. Moreover, little is known about the genomic consequences of this recent demographic bottleneck or the impact on its evolutionary potential. A comparison of historical and modern genomes would thus allow us to understand the genomic consequences of this severe human-induced decline. Novel genomic techniques provide the opportunity to quantify these effects and to track changes in inbreeding and harmful mutations in real time. Here, we propose to sequence historical genomes of the Baltic Proper harbour porpoise, sampled before the severe population decline of the mid-20th century. These will be compared with available modern samples already sequenced by the team, in order to (i) reconstruct the population’s demographic history, (ii) investigate genomic consequences of the recent demographic bottleneck, and predict its future recovery. Comparing genomic variation in historical museum samples with modern ones, using newly-generated next generation sequencing techniques provides a rare opportunity to track micro-evolutionary processes in a critically endangered population, in real time. This project will build on our expertise in museomics and conservation genomics of arctic fox and other critically endangered species. The results generated in this study will be published in high impact international peer-reviewed journals.