Many marine pelagic fish species are characterized by subtle but complex genetic structures and dynamics, depending on the balance between current-mediated larval dispersal and adult active homing behavior. The circumantarctic continuous hydrodynamics of the Southern Ocean is a prime example of a system with a potentially great homogenizing effect among distant populations. We tested this hypothesis by analyzing the contemporary genetic relatedness among populations of a common and endemic mesopelagic fish of the Southern Ocean, Electrona antarctica. Seven newly developed species-specific microsatellite markers were used to investigate patterns of neutral genetic variation in 11 geographically widespread samples (n=400) collected between 2006 and 2007. We detected a very high level of genetic diversity, but a striking lack of genetic differentiation on a circumantarctic scale, indicating large effective population sizes complemented with high levels of admixture. These findings underscore the large scale homogenizing effect of the Southern Coastal Current, leading to a high level of connectivity of our model species in the Southern Ocean, which is congruent with its huge biomass and central role in marine food webs. As an important Antarctic marine living resource this species may as such be managed on a circumantarctic level, although the demographic stability of this stock should be estimated urgently.