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Marine fish seem to experience evolutionary processes that are expected to produce genetically homogeneous populations. We have assessed genetic diversity and differentiation in 15 samples of the sand goby Pomatoschistus minutus (Pallas, 1770) (Gobiidae, Teleostei) from four major habitats within the Southern Bight of the North Sea, using seven microsatellite and 13 allozyme loci. Despite its high dispersal potential, microsatellite loci revealed a moderate level of differentiation (overall FST= 0.026; overall RST= 0.058). Both hierarchical analysis of molecular variance and multivariate analysis revealed significant differentiation (P< 0.01) between estuarine, coastal and marine samples with micro-satellites, but not with allozymes. Comparison among the different estimators of differentiation (FST and RST) pointed to possible historical events and contemporary habitat fragmentation. Samples were assigned to two breeding units in the estuary and coastal region. Despite this classification, there were indications of a complex and dynamic spatiotemporal structure, which is, most likely, determined by historical events and local oceanic currents. [ABSTRACT FROM AUTHOR]