Populations of beaked whales are subject to natural and anthropogenic impacts. This study will quantify the extent to which repetitive anthropogenic impacts may have long-term, population-level effects such as reductions in genetic variability and/or changes in population and social structure of affected populations. We take a comparative approach to evaluate the potential for population-level effects of naval activities on paired ‘disturbed’ and ‘semi-pristine’ populations of beaked whales in three different regions: Canary Islands, Bahamas and the Mediterranean. Life-history traits, social structure, social cohesion and genetic diversity play an important role in the persistence and resilience of cetacean populations. Firstly we will evaluate these traits in semi-pristine areas: the little disturbed Cuvier’s (Ziphius cavirostris) and Blainville’s (Mesoplodon densirostris) beaked whale populations off the island of El Hierro (western Canary Islands) and the semi-disturbed population of Cuvier’s beaked whale in the Ligurian Sea (Mediterranean). The results will be related to similar on-going research in the island of Abaco (Bahamas). This part of the study builds on a NOPP-ONR funded long-term photoID data series of these species off El Hierro (www.cetabase.info), expands this dataset and adds biopsy sampling. Also, the project builds on existing photoID and biopsy data from the Ligurian Sea. Genetic diversity will be assessed using single nucleotide polymorphisms (SNPs) derived from restriction associated digest (RAD) tag sequencing, and constructing DNA profiles comprising genetically identified sex, mitochondrial genome sequences and SNP genotypes. Secondly, these analyses will be applied to skin samples gathered from highly impacted beaked whale populations. This includes the eastern Canary Islands and the Ionian Sea, where several mass-strandings of beaked whales related to sonar have been recorded from 1983 to 2004 (Canary Islands), and up to 2013 (Ionian). Existing genetic data from the AUTEC naval range and the little-impacted island of Abaco, in Bahamas, are available for comparative analysis. Paired-site analysis will allow us to compare the genetic diversity and social structure of impacted and little or non-impacted populations of beaked whales in the three regions. Finally, we will place these results in the context of a global study of genetic diversity and population structure. This will be done using full mitochondrial genome sequences and SNP genotypes generated from a collection of samples of Blainville’s and Cuvier’s from around the world. The matched-site comparative approach, in the context of a global genetic study of the species under examination, provides a powerful approach to test hypotheses on the relationship between anthropogenic impact, social structure and genetic diversity.