The spatial structuring of intraspecific genetic diversity is the result of random genetic drift, natural selection, migration, mutation, and their interaction with historical processes. The contribution of each has been typically difficult to estimate, but recent advances in statistical genetics have provided valuable new investigative tools to tackle such complexity. Using a combination of such methods, we examined the roles of environment (i.e., natural selection), random genetic processes (i.e., drift), and demography and life histories (e.g., feeding migrations) on population structure of a widely distributed and abundant marine pelagic fish of economic importance, Atlantic herring (Clupea harengus). Individuals were collected during peak spawning time from 19 spawning locations spanning the region from the western North Sea to the eastern Baltic Sea (N= 1859, eight microsatellite loci). We carried out separate analyses of neutral and selected genetic variation, which allowed us to establish that the two most important factors affecting population structure were selection due to salinity at spawning sites and feeding migrations. The genetic signal left by the demographic history of herring, on the other hand, seems to have been largely eroded, which is not surprising given the large reproductive potential and presumed enormous local effective population sizes of pelagic fish that constrain the effect of stochastic processes. The approach we used can in principle be applied to any abundant and widely distributed aquatic or terrestrial species.