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 ago, 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. 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 allow for quantifying these effects and tracking 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, 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.