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Zarraonaindia, I., Pardo, M. A., Iriondo, M., Manzano, C., and Estonba, A. 2009. Microsatellite variability in European anchovy (Engraulis encrasicolus) calls for further investigation of its genetic structure and biogeography. – ICES Journal of Marine Science, 66: 2176–2182. Attention to genetic and ecological perspectives can enhance strategies for using fishery resources sustainably. A potentially important application is the use of molecular markers to assess the genetic stock structure of a harvested species. In this study, seven microsatellite markers were analysed in anchovy samples from the Bay of Biscay, the Gulf of Cádiz, and the Gulf of Lions to assess the genetic structure of anchovy (Engraulis encrasicolus) populations in the Bay of Biscay and to infer the biogeographic origin of these populations. All samples showed a deficit of heterozygotes that could be explained by non-random mating, Wahlund's effect, and especially by the presence of null alleles. Global FST and RST values, uncorrected and corrected for null alleles, were significant. There was significant genetic heterogeneity between two populations in the Bay of Biscay, suggesting that anchovy there may not be panmictic. Moreover, the results reinforce the hypothesis of a recent common ancestor shared by Bay of Biscay and western Mediterranean anchovy. These results, together with those of earlier studies, suggest merit in further investigating spatio-temporal genetic variation among anchovy populations in the Northeastern Atlantic.