The Monachinae, or southern seals, are one of two subfamilies within the Phocidae, and are home to iconic pinnipeds such as the leopard seal, a fierce Antarctic top predator, and the Mediterranean monk seal, one of the world's most endangered mammals. These two species are difficult to study and sample, due to their hidden lives in extreme environments or, in case of the monk seal, their critically reduced population sizes, consequently genetic data from these two species is scarce. However, cost developments and advances in genome sequencing have made it possible to generate continuous genome assemblies from DNA of even stranded individuals, allowing to assemble the first reference genomes of such rarely observed species.</p><p>In this study, we have sequenced the genomes of the leopard seal and the Mediterranean monk seal using PacBio's CCS technology to assemble the very first genomes for these species. Four additional Mediterranean monk seal individuals were sequenced using Illumina short-read technology. These data allowed analysis of their demography and genomic diversity based on whole-genome data, confirming low genetic variability and small numbers of individuals for the Mauretanian population of the Mediterranean monk seal. In contrast, the relatively abundant leopard seal shows a high degree of heterozygosity, comparable in the range of other common carnivores.</p><p>The first genome assemblies for these seals will lay the groundwork for population-level and other studies to better understand their evolutionary history and biology, and to aid conservation efforts.