There is a growing consensus that much of the contemporary phylogeography of northern hemisphere coastal taxa reflects the impact of Pleistocene glaciation, when glaciers covered much of the coastline at higher latitudes and sea levels dropped by as much as 150 m. The genetic signature of postglacial recolonization has been detected in many marine species, but the effects of coastal glaciation are not ubiquitous, leading to suggestions that species may intrinsically differ in their ability to respond to the environmental change associated with glacial cycles. Such variation may indeed have a biological basis, but apparent differences in population structure among taxa may also stem from our heavy reliance on individual mitochondrial loci, which are strongly influenced by stochasticity during coalescence. We investigated the contemporary population genetics of Syngnathus typhle, one of the most widespread European coastal fish species, using a multilocus data set to investigate the influence of Pleistocene glaciation and reduced sea levels on its phylogeography. A strong signal of postglacial recolonization was detected at both the northern and eastern ends of the species’ distribution, while southern populations appear to have been relatively unaffected by the last glacial cycle. Patterns of population variation and differentiation at nuclear and mitochondrial loci differ significantly, but simulations indicate that these differences can be explained by the stochastic nature of the coalescent process. These results demonstrate the strength of a multilocus approach to phylogeography and suggest that an overdependence on mitochondrial loci may provide a misleading picture of population-level processes.