There has been a long-term interest in the population genetics of Antarctic krill species because of their ecological and economic importance. The possibility that there are distinct genetic stocks of these species would affect the design of management strategies for their conservation. A recent resurgence of interest in identifying distinct stocks of swarming krill species has been driven by the development of genetic technologies that are more sensitive to subtle population structure than older methods. Previous studies of the population genetics of the Antarctic species Euphausia crystallorophias and E. superba and the boreal species Meganyctiphanes norvegica that used allozymes found no evidence of genetic population structure. More recent investigations using sequence variation in mitochondrial DNA (mtDNA) have exposed genetic differentiation between samples taken from different parts of each species’ range. However, the underlying assumption of these studies that differentiation between samples is caused primarily by restricted gene flow between widely separated sampling sites may be incorrect. Our recent study of E. crystallorophias mtDNA variation has indicated that there is significant genetic differentiation between samples taken within one region. This has important implications for the design of future studies of krill population genetics, which must be able to accommodate this sympatric variance component as well as variance attributable to differences between regions. Genetic differentiation between stocks of krill in different regions therefore can not be adequately assessed unless multiple samples are taken from each region.