Genetic differentiation among juvenile samples of the European seabass (Dicentrarchus labrax) from the coast of Portugal is reported by means of two types of genetic markers: allozymes and microsatellites. Repeat samples were taken from 5 different nursery grounds (Aveiro, Foz, Obidos, Milfontes and Faro) along the coast of Portugal between November 1992 and February 1994. Starch-gel electrophoresis was used to assess the level and distribution of genetic variability of 38 loci. Six of these were found to be polymorphic at the 99% level and were used in population surveys: AAT-3*, ADA *, GPI-I *, GPI-2*, G3PDH-2*, SOD*. Statistical analysis revealed low but statistically significant multilocus F.'I (0.0108, p<O.OOI) values suggesting that population structuring exists along the Portuguese coast line. The results indicate that there is some restriction in gene flow between the more southerly population at Faro and all other sites to the North. Five microsatellite loci were screened in over 300 individuals. High levels of polymorphism (number of alleles observed per locus ranged from 20 to 41) and observed heterozygosities, ranging from 0.45 to 0.89 (mean over all loci = 0.71) were detected. Two loci displayed heterozygosity deficits (Dla6 and Labrax-9) and were not used in population comparisons. Statistical analysis revealed low but statistically significant multilocus FST (0.0025, p<O.OOl) at the other three loci (Dlall, Labrax-3 and Labrax-8). No clear geographic patterns emerged from these results. Overall allozymes performed well when compared to microsatellites, in detecting microgeographic genetic structure in this species. Microsatellites revealed high levels of polymorphism that should prove useful as markers in the management of wild and farmed seabass stocks in the future. The level of differentiation, low values of F ST , detected among the sites is low but is typical of marine species which have a much greater chance of mixing.