<p>Effective conservation of cryptic marine species depends on a sound understanding of genetic diversity, population structure and connectivity. These data allow for the delineation of conservation units and assessment of extinction risk and are especially valuable for species with fragmented distributions or suspected regional endemism. The Bryde’s whale (<i>Balaenoptera edeni</i>) exemplifies a challenge, being a poorly understood baleen whale species globally, with a complex of resident inshore and migratory offshore populations across temperate and sub-tropical waters. One such is the inshore population that inhabits South African coastal waters, where it is classified nationally as Vulnerable (D1) due to its small population size. This study uses a panel of 14 microsatellite markers and mitochondrial DNA control region sequences to advance our understanding of the genetic isolation and extinction risk of this population, informing the delineation of conservation units and guiding population-specific management actions. Results indicate that this population is characterized by moderate nuclear microsatellite and low mitochondrial DNA diversity and preliminarily indicate genetic differentiation between populations in the southern African region. On a global scale the findings show differentiation between broad ocean regions and the SAi while supporting the difference in evolutionary origin of SAi and SEA. These findings underscore the need for active conservation management for this isolated coastal population since they provide genetic evidence for the recognition of a discrete management unit. It is recommended that further refinement in understanding of the population’s evolutionary distinctiveness will strengthen conservation assessments, support listing decisions, and guide targeted management interventions.</p>