Heaviside's dolphin, Cephalorhynchus heavisidii, is endemic to coastal waters of the western seaboard of South Africa and Namibia. The inshore habitat of the species places it at risk from commercial fishing operations and has led to concerns that the depletion of regional populations may result in loss of locally adapted genetic variation. To determine the geographic population structure of the Heaviside's dolphin, we obtained control region sequence (HVR1) from 17 specimens collected along the South African west coast and 18 animals taken along the Namibian coast. We identified 17 unique haplotypes within these 35 specimens which were aligned to 18 HVR1 sequences available from 40 specimens deposited in Genbank. A total of 20 maternal haplotypes was detected in the combined sample of 75 animals, of which ten were singletons. Neighbour joining and parsimony methods showed an absence of correspondence between group structure and geographic locality. Analysis of molecular variance (AMOVA) showed that almost all of the genetic variation is attributable to variation within geographic regions. This low level of differentiation between South Africa and Namibia is further underscored by an extremely low ϕST value suggestive of genetic homogeneity within the species. However, we caution that the failure to detect unambiguous population structure genetically does not necessarily mean that the population should be considered one panmictic unit for management purposes. Our genetic results should not be viewed in isolation but be considered in combination with information from nuclear markers, morphometrics, pollutants and tagging studies.