The synergistic effects of anthropogenic stressors have led to the degradation of Earth's biodiversity and rapid disappearance of species from the tree of life, leading to the suggestion we are currently undergoing a sixth mass extinction. Although most of these extinctions are observed in the terrestrial realm, marine extinction rates may have been underestimated due to low rates of species discovery, taxonomic description and conservation assessment of marine species. Moreover, many marine populations have undergone drastic population declines and or extinctions at local or regional scales, leading to widespread disruption of ecological networks. Thus, it is of the utmost importance to document marine biodiversity and establish baseline data to inform conservation strategies. Marine mammals are no exception to these threats, and several species are at risk of extinction. For instance, in recent history, the North Atlantic gray whale (Eshcrichtius robustus) has disappeared from an entire ocean basin and the reason for its demise remains much of a mystery. Extant gray whales are primarily coastal migrators, giving biologists the opportunity to gather population estimates and life history information to inform conservation assessments. Other cetaceans, such as beaked whales, are so rare that they are known only from a handful of incomplete skeletons, meaning there is very little information about beaked whale population structure, genomic diversity or how they respond to changing climate change and anthropogenic stressors. To better understand how marine mammals may respond to modern anthropogenic and climatic stressors and contribute to the baseline data on marine species, the aims of this thesis are threefold: (i) infer the speciation process of three Berardius species (ii) describe a new Mesoplodon species of beaked whale and (iii) investigate the demise of North Atlantic gray whales. Following an Introduction of relevant background information and project aims, I present the three main chapters of this thesis. The first chapter explores the species designation of the recently described Sato’s beaked whale (B. minimus) and documents the evolutionary history and speciation process of all three Berardius beaked whales using whole nuclear and mitochondrial genomes. In the second chapter, we propose the delineation of a new species, Ramari’s beaked whale (Mesoplodon eueu), based on morphological and genomic (ddRAD, nuclear and mitochondrial genomes) data. The third chapter documents the decline of North Atlantic gray whales and infers the evolutionary relationship between North Atlantic and North Pacific populations using both modern and ancient North Pacific and ancient North Atlantic mitogenomes. The thesis demonstrates the value of using genome data to enlighten our understanding of marine speciation processes, and provides inspiration and directions for future studies of marine biodiversity.